1
|
Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS OMEGA 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
Collapse
Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| |
Collapse
|
2
|
Staii C. Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy. Molecules 2023; 28:4632. [PMID: 37375186 DOI: 10.3390/molecules28124632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM-force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function.
Collapse
Affiliation(s)
- Cristian Staii
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA
| |
Collapse
|
3
|
Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
4
|
Bhuin S, Halder S, Saha SK, Chakravarty M. Binding interactions and FRET between bovine serum albumin and various phenothiazine-/anthracene-based dyes: a structure-property relationship. RSC Adv 2021; 11:1679-1693. [PMID: 35424090 PMCID: PMC8693680 DOI: 10.1039/d0ra09580j] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
The present study demonstrates binding interactions and Förster resonance energy transfer (FRET) between bovine serum albumin (BSA) and a series of structurally and electronically diverse phenothiazine (PTZ) and anthracene (ANT) dyes. Upon selective excitation of tryptophan (Trp) residues of BSA, radiationless energy transfer to a dye takes place, resulting in fluorescence quenching of the former. Fluorescence quenching mechanisms, FRET parameters, possible locations, and binding constants of dyes with the BSA have been examined to deduce a structure–property relationship. The mechanism of quenching is apparently static in nature. PTZ dyes with heteroatoms and a pentyl tail (C5-PTZ) attached to them were found to have a stronger binding affinity with BSA as compared to ANT dyes. Stronger binding affinities of C5-PTZ dyes with BSA result in greater energy transfer efficiencies (ET). A dye with a strong electron-withdrawing group present in it has shown better energy accepting capability. A FRET study with dicyanoaniline (DCA) analogs of PTZ and ANT dyes (C5-PTZDCA and ANTDCA, respectively) revealed that ET depends on electronic and structural factors of molecules. An almost orthogonal geometry between ANT and DCA moieties (∼79°) in ANTDCA induces the greater extent of electron transfer from ANT to DCA, showing a higher ET for this dye as compared to C5-PTZDCA in which the torsion angle is only ∼38°. Further, the observed facts have been validated by experimentally determined bandgaps (using cyclic voltammetry experiments) for all the dyes. Thus, the hydrophobic character and the presence of interactive substituents along with the electron-accepting abilities majorly control the FRET for such dyes with BSA. The present study demonstrates binding interactions and Förster resonance energy transfer (FRET) between bovine serum albumin (BSA) and a series of structurally and electronically diverse phenothiazine (PTZ) and anthracene (ANT) dyes.![]()
Collapse
Affiliation(s)
- Shouvik Bhuin
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Sayantan Halder
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Subit Kumar Saha
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Manab Chakravarty
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| |
Collapse
|
5
|
Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer. ACS NANO 2020; 14:5956-5967. [PMID: 32216328 DOI: 10.1021/acsnano.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.
Collapse
Affiliation(s)
- Corentin Léger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Akram Yahia-Ammar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
| |
Collapse
|
6
|
Tankasala D, Linnes JC. Noninvasive glucose detection in exhaled breath condensate. Transl Res 2019; 213:1-22. [PMID: 31194942 PMCID: PMC6783357 DOI: 10.1016/j.trsl.2019.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/02/2019] [Accepted: 05/26/2019] [Indexed: 01/04/2023]
Abstract
Two-thirds of patients with diabetes avoid regularly monitoring their blood glucose levels because of the painful and invasive nature of current blood glucose detection. As an alternative to blood sample collection, exhaled breath condensate (EBC) has emerged as a promising noninvasive sample from which to monitor glucose levels. However, this dilute sample matrix requires sensors capable of detecting glucose with high resolution at nanomolar and micromolar concentrations. Recent developments in EBC collection methods and highly sensitive glucose biosensors provide a path toward enabling robust and sensitive glucose detection in EBC. This review addresses current and emerging EBC collection and glucose sensing modalities capable of quantifying glucose in EBC samples. We highlight the opportunities and challenges for development and integration of EBC glucose detection systems that will enable clinically robust and accurate EBC glucose measurements for improved glycemic control.
Collapse
Affiliation(s)
- Divya Tankasala
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.
| |
Collapse
|
7
|
Field LD, Walper SA, Susumu K, Lasarte-Aragones G, Oh E, Medintz IL, Delehanty JB. A Quantum Dot-Protein Bioconjugate That Provides for Extracellular Control of Intracellular Drug Release. Bioconjug Chem 2018; 29:2455-2467. [DOI: 10.1021/acs.bioconjchem.8b00357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lauren D. Field
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Guillermo Lasarte-Aragones
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- George Mason University, College of Sciences, Fairfax, Virginia 22030 United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - James B. Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| |
Collapse
|
8
|
Lai WF, Rogach AL, Wong WT. Chemistry and engineering of cyclodextrins for molecular imaging. Chem Soc Rev 2018; 46:6379-6419. [PMID: 28930330 DOI: 10.1039/c7cs00040e] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclodextrins (CDs) are naturally occurring cyclic oligosaccharides bearing a basket-shaped topology with an "inner-outer" amphiphilic character. The abundance of hydroxyl groups enables CDs to be functionalized with multiple targeting ligands and imaging elements. The imaging time, and the payload of different imaging elements, can be tuned by taking advantage of the commercial availability of CDs with different sizes of the cavity. This review aims to offer an outlook of the chemistry and engineering of CDs for the development of molecular probes. Complexation thermodynamics of CDs, and the corresponding implications for probe design, are also presented with examples demonstrating the structural and physiochemical roles played by CDs in the full ambit of molecular imaging. We hope that this review not only offers a synopsis of the current development of CD-based molecular probes, but can also facilitate translation of the incremental advancements from the laboratory to real biomedical applications by illuminating opportunities and challenges for future research.
Collapse
Affiliation(s)
- Wing-Fu Lai
- School of Pharmaceutical Sciences, Health Science Centre, Shenzhen University, Shenzhen, China.
| | | | | |
Collapse
|
9
|
Mujoo H, Reynolds JNJ, Tucker IG. A real-time in vitro assay to evaluate the release of macromolecules from liposomes. Drug Test Anal 2017; 10:1025-1032. [PMID: 29088510 DOI: 10.1002/dta.2332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022]
Abstract
The availability of a real-time assay to experimentally investigate the release of encapsulated proteins would be beneficial given the interest in the use of liposomes as a drug delivery vehicle. Although simple assays for small molecular weight substances exist, assays to evaluate macromolecules do not. Here we describe a method that detects the release of model macromolecules from liposomes in real time. The assay employs the intermolecular distance-dependent phenomenon of fluorescence resonance energy transfer (FRET) between the fluorophore donor, fluorescein (FITC), and fluorescent quencher, QSY® 9. The macromolecular species were conjugated to the markers fluorescein (44kDa dextran) and QSY® 9 (67 kDa bovine serum albumin, BSA). Following confirmation of quenching between FITC-Dex and QSY® 9-BSA, liposomes were loaded with the macromolecular markers and subjected to various treatments (high-pressure extrusion and Triton X solubilisation) to cause release from liposomes. An increase in FITC fluorescence was observed when liposomes were subjected to extrusion cycles. Surprisingly, the addition of Triton X did not cause an increase in fluorescence probably because the FRET pair became associated with mixed micelles. This assay method should be useful in studies to investigate the mechanisms by which macromolecules are released from liposomes, particularly when liposomes are exposed to release-triggers (eg, temperature change, pH change, ultrasound). Such understanding will underpin the formulation of triggered liposomal delivery systems for macromolecules.
Collapse
Affiliation(s)
- Himang Mujoo
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - John N J Reynolds
- Department of Anatomy, The Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Ian G Tucker
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| |
Collapse
|
10
|
Rosa LT, Dix SR, Rafferty JB, Kelly DJ. Structural basis for high-affinity adipate binding to AdpC (RPA4515), an orphan periplasmic-binding protein from the tripartite tricarboxylate transporter (TTT) family in Rhodopseudomonas palustris. FEBS J 2017; 284:4262-4277. [PMID: 29082669 DOI: 10.1111/febs.14304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 01/24/2023]
Abstract
The tripartite tricarboxylate transporter (TTT) family is a poorly characterised group of prokaryotic secondary solute transport systems, which employ a periplasmic substrate-binding protein (SBP) for initial ligand recognition. The substrates of only a small number of TTT systems are known and very few SBP structures have been solved, so the mechanisms of SBP-ligand interactions in this family are not well understood. The SBP RPA4515 (AdpC) from Rhodopseudomonas palustris was found by differential scanning fluorescence and isothermal titration calorimetry to bind aliphatic dicarboxylates of a chain length of six to nine carbons, with KD values in the μm range. The highest affinity was found for the C6-dicarboxylate adipate (1,6-hexanedioate). Crystal structures of AdpC, either adipate or 2-oxoadipate bound, revealed a lack of positively charged amino acids in the binding pocket and showed that water molecules are involved in bridging hydrogen bonds to the substrate, a conserved feature in the TTT SBP family that is distinct from other types of SBP. In AdpC, both of the ligand carboxylate groups and a linear chain conformation are needed for coordination in the binding pocket. RT-PCR showed that adpC expression is upregulated by low environmental adipate concentrations, suggesting adipate is a physiologically relevant substrate but as adpC is not genetically linked to any TTT membrane transport genes, the role of AdpC may be in signalling rather than transport. Our data expand the known ligands for TTT systems and identify a novel high-affinity binding protein for adipate, an important industrial chemical intermediate and food additive. DATABASES Protein structure co-ordinates are available in the PDB under the accession numbers 5OEI and 5OKU.
Collapse
Affiliation(s)
- Leonardo T Rosa
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Samuel R Dix
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| |
Collapse
|
11
|
Benkovics G, Malanga M, Fenyvesi É. The ‘Visualized’ macrocycles: Chemistry and application of fluorophore tagged cyclodextrins. Int J Pharm 2017; 531:689-700. [DOI: 10.1016/j.ijpharm.2017.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/06/2017] [Accepted: 04/16/2017] [Indexed: 12/22/2022]
|
12
|
Mitchell JA, Whitfield JH, Zhang WH, Henneberger C, Janovjak H, O’Mara ML, Jackson CJ. Rangefinder: A Semisynthetic FRET Sensor Design Algorithm. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Mitchell
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Jason H. Whitfield
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - William H. Zhang
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Christian Henneberger
- Institute
of Neurology, University College London, London, WC1E 6BT, United Kingdom
- German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
- Institute
of Cellular Neurosciences, University of Bonn, 53113 Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Megan L. O’Mara
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| |
Collapse
|
13
|
Sansalone L, Tang S, Zhang Y, Thapaliya ER, Raymo FM, Garcia-Amorós J. Semiconductor Quantum Dots with Photoresponsive Ligands. Top Curr Chem (Cham) 2016; 374:73. [DOI: 10.1007/s41061-016-0073-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/15/2016] [Indexed: 10/20/2022]
|
14
|
Mattoussi H, Medintz IL, Clapp AR, Goldman ER, Jaiswal JK, Simon SM, Mauro JM. Luminescent Quantum Dot-Bioconjugates in Immunoassays, FRET, Biosensing, and Imaging Applications. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/s1535-5535-03-00083-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Colloidal semiconductor nanocrystals (quantum dots, QDs), such as CdSe-ZnS core-shell, are highly luminescent and stable inorganic fluorophores that represent a promising alternative to organic dyes for a variety of biotechnological applications. They show size-tunable narrow photoluminescence spectra spanning nearly the full visible region of the optical spectrum for QDs with CdSe cores. We have developed several approaches to conjugate either one type or a combination of biologically distinct proteins to CdSe-ZnS core-shell QDs rendered water-soluble by surface ligation with dihydrolipoic acid (DHLA) groups. QD-protein conjugates prepared using these approaches were found to exhibit high specificity and stability in immunoassays and in Förster resonance energy transfer (FRET) assays as well as in prototype QD bioconjugate sensors. Tunable QD emission over a wide range of wavelengths permitted effective tuning of the degree of energy overlap between the QD donor and an acceptor dye, allowing control over the rate of FRET. Additionally, we have used these QD-bioconjugates in live cell labeling. These hybrid bioinorganic conjugates represent a promising tool for use in many biotechnological applications.
Collapse
Affiliation(s)
- Hedi Mattoussi
- Division of Optical Sciences, U.S. Naval Research Laboratory
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory
| | - Aaron R. Clapp
- Division of Optical Sciences, U.S. Naval Research Laboratory
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory
| | | | | | - J. Matthew Mauro
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory
| |
Collapse
|
15
|
Kim EM, Jeong HJ. Current Status and Future Direction of Nanomedicine: Focus on Advanced Biological and Medical Applications. Nucl Med Mol Imaging 2016; 51:106-117. [PMID: 28559935 DOI: 10.1007/s13139-016-0435-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/18/2016] [Accepted: 07/01/2016] [Indexed: 02/06/2023] Open
Abstract
Nanotechnology is the engineering and manipulation of materials and devices with sizes in the nanometer range. Colloidal gold, iron oxide nanoparticles and quantum dot semiconductor nanocrystals are examples of nanoparticles, with sizes generally ranging from 1 to 20 nm. These nanotechnologies have been researched tremendously in the last decade and this has led to a new area of "nanomedicine" which is the application of nanotechnology to human health-care for diagnosis, monitoring, treatment, prediction and prevention of diseases. Recently progress has been made in overcoming some of the difficulties in the human use of nanomedicines. In the mid-1990s, Doxil was approved by the FDA, and now various nanoconstructs are on the market and in clinical trials. However, there are many obstacles in the human application of nanomaterials. For translation to clinical use, a detailed understanding is needed of the chemical and physical properties of particles and their pharmacokinetic behavior in the body, including their biodistribution, toxicity, and biocompatibility. In this review, we provide a broad introduction to nanomedicines and discuss the preclinical and clinical trials in which they have been evaluated.
Collapse
Affiliation(s)
- Eun-Mi Kim
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Chonbuk National University Medical School and Hospital, Jeonju-si, Jellaabuk-Do Republic of Korea
| | - Hwan-Jeong Jeong
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Chonbuk National University Medical School and Hospital, Jeonju-si, Jellaabuk-Do Republic of Korea
| |
Collapse
|
16
|
Edwards KA, Seog WJ, Han L, Feder S, Kraft CE, Baeumner AJ. High-Throughput Detection of Thiamine Using Periplasmic Binding Protein-Based Biorecognition. Anal Chem 2016; 88:8248-56. [PMID: 27460839 DOI: 10.1021/acs.analchem.6b02092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although antibodies and aptamers are commonly used bioaffinity recognition elements, they are not available for many important analytes. As an alternative, we demonstrate use of a periplasmic binding protein (PBP) to provide high affinity recognition for thiamine (vitamin B1), an analyte of great importance to human and environmental health for which, like so many other small molecules, no suitable biorecognition element is available. We demonstrate that with an appropriate competitive strategy, a highly sensitive (limit of detection of 0.5 nM) and specific bioassay for thiamine and its phosphorylated derivatives can be designed. The high-throughput method relies upon the thiamine periplasmic binding protein (TBP) from Escherichia coli for thiamine biorecognition and dye-encapsulating liposomes for signal-enhancement. A thiamine monosuccinate-PEG-biotin derivative was synthesized to serve as an immobilized competitor that overcame constraints imposed by the deep binding cleft and structural recognition requirements of PBPs. The assay was applied to ambient environmental samples with high reproducibility. These findings demonstrate that PBPs can serve as highly specific and sensitive affinity recognition elements in bioanalytical assay formats, thereby opening up the field of affinity sensors to a new range of analytes.
Collapse
Affiliation(s)
- Katie A Edwards
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| | - Woo Jin Seog
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| | - Lu Han
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| | - Seth Feder
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| | - Clifford E Kraft
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| | - Antje J Baeumner
- Departments of †Natural Resources, ‡Biological and Environmental Engineering, §Food Science, and ∥Chemical Engineering, Cornell University , Ithaca, New York, United States
| |
Collapse
|
17
|
Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
| | | | | |
Collapse
|
18
|
Russo A, Scognamiglio PL, Hong Enriquez RP, Santambrogio C, Grandori R, Marasco D, Giordano A, Scoles G, Fortuna S. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands. PLoS One 2015; 10:e0133571. [PMID: 26252476 PMCID: PMC4529233 DOI: 10.1371/journal.pone.0133571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Abstract
Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
Collapse
Affiliation(s)
- Anna Russo
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Medical Biotechnology, University of Siena, Policlinico Le Scotte, Viale Bracci, Siena, Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
| | | | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
- * E-mail: (SF); (DM)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine & Center for Biotechnology Temple University Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Surgery & Neuroscience University of Siena, Strada delle Scotte n. 6, Siena, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sara Fortuna
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- * E-mail: (SF); (DM)
| |
Collapse
|
19
|
QIN CG, LU CX, OUYANG GW, QIN K, ZHANG F, SHI HT, WANG XH. Progress of Azobenzene-based Photoswitchable Molecular Probes and Sensory Chips for Chemical and Biological Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60809-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
20
|
Zrazhevskiy P, Dave SR, Gao X. Addressing Key Technical Aspects of Quantum Dot Probe Preparation for Bioassays. PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION : MEASUREMENT AND DESCRIPTION OF PARTICLE PROPERTIES AND BEHAVIOR IN POWDERS AND OTHER DISPERSE SYSTEMS 2014; 31:1291-1299. [PMID: 26207082 PMCID: PMC4507434 DOI: 10.1002/ppsc.201400184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Indexed: 05/05/2023]
Abstract
Fluorescent semiconductor nanoparticles, or quantum dots, have become a promising platform for the engineering of biofunctional probes for a variety of biomedical applications, ranging from multicolor imaging to single-molecule tracking to traceable drug delivery. Advances in organometallic synthesis have enabled preparation of hydrophobic quantum dots with high quantum yields and narrow size distribution, offering bright optical materials with narrow size-tunable emission profiles. At the same time, polymer encapsulation procedures provided a simple and versatile methodology for transferring hydrophobic nanoparticles into physiologically-relevant aqueous buffers. Taken together, hydrophobic nanoparticle platforms and polymer encapsulation should offer great flexibility for implementation of novel probe designs. However, the success of the encapsulation and purification depends on many factors often overlooked in the scientific literature, such as close match between nanoparticle and polymer physicochemical properties and dimensions, slow dynamics of polymer arrangement on the nanoparticle surface, and the size and charge similarity of resultant polymer-coated quantum dots and empty byproduct polymer micelles. To make this general hydrophobic nanoparticle modification strategy accessible by a broad range of biomedical research groups, we focus on the important technical aspects of nanoparticle polymer encapsulation, purification, bioconjugation, and characterization.
Collapse
Affiliation(s)
- Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Shivang R. Dave
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
21
|
Liu W, Kavaliauskas D, Schrader JM, Poruri K, Birkedal V, Goldman E, Jakubowski H, Mandecki W, Uhlenbeck OC, Knudsen CR, Goldman YE, Cooperman BS. Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation. ACS Chem Biol 2014; 9:2421-31. [PMID: 25126896 PMCID: PMC4201349 DOI: 10.1021/cb500409y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The universally conserved translation
elongation factor EF-Tu delivers
aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary
complex (TC) to the ribosome where it binds to the cognate mRNA codon
within the ribosomal A-site, leading to formation of a pretranslocation
(PRE) complex. Here we describe preparation of QSY9 and Cy5 derivatives
of the variant E348C-EF-Tu that are functional in translation elongation.
Together with fluorophore derivatives of aa-tRNA and of ribosomal
protein L11, located within the GTPase associated center (GAC), these
labeled EF-Tus allow development of two new FRET assays that permit
the dynamics of distance changes between EF-Tu and both L11 (Tu-L11
assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding
process. We use these assays to examine: (i) the relative rates of
EF-Tu movement away from the GAC and from aa-tRNA during decoding,
(ii) the effects of the misreading-inducing antibiotics streptomycin
and paromomycin on tRNA selection at the A-site, and (iii) how strengthening
the binding of aa-tRNA to EF-Tu affects the rate of EF-Tu movement
away from L11 on the ribosome. These FRET assays have the potential
to be adapted for high throughput screening of ribosomal antibiotics.
Collapse
Affiliation(s)
| | | | - Jared M. Schrader
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Kiran Poruri
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | | | - Emanuel Goldman
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Hieronim Jakubowski
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Wlodek Mandecki
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Olke C. Uhlenbeck
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | | |
Collapse
|
22
|
Ozyurt C, Evran S, Telefoncu A. Development of genetically encoded fluorescent protein constructs of hyperthermophilic maltose-binding protein. Prep Biochem Biotechnol 2014; 44:132-45. [PMID: 24152100 DOI: 10.1080/10826068.2013.797436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Circularly permuted green fluorescent protein (cGFP) was inserted into the hyperthermophilic maltose binding protein at two different locations. cGFP was inserted between amino acid residues 206 and 207, or fused to the N-terminal of maltose binding protein from Thermotoga maritima. The cloned DNA constructs were expressed in Escherichia coli cells, and purified by metal chelate affinity chromatography. Conformational change upon ligand binding was monitored by the increase in fluorescence intensity. Both of the fusion proteins developed significant fluorescence change at 0.5 mM maltose concentration, whereas their maltose binding affinities and optimum incubation times were different. Fluorescent biosensors based on mesophilic maltose binding proteins have been described in the literature, but there is a growing interest in biosensors based on thermostable proteins. Therefore, the developed protein constructs could be models for thermophilic protein-based fluorescent biosensors.
Collapse
Affiliation(s)
- Canan Ozyurt
- a Department of Biochemistry, Faculty of Science , Ege University , Izmir , Turkey
| | | | | |
Collapse
|
23
|
Feng L, Zhu A, Wang H, Shi H. A nanosensor based on quantum-dot haptens for rapid, on-site immunoassay of cyanotoxin in environmental water. Biosens Bioelectron 2014; 53:1-4. [DOI: 10.1016/j.bios.2013.09.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/01/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
|
24
|
Blanco-Canosa JB, Wu M, Susumu K, Petryayeva E, Jennings TL, Dawson PE, Algar WR, Medintz IL. Recent progress in the bioconjugation of quantum dots. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.08.030] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Chouhan RS, Qureshi A, Niazi JH. Quantum dot conjugated S. cerevisiae as smart nanotoxicity indicators for screening the toxicity of nanomaterials. J Mater Chem B 2014; 2:3618-3625. [DOI: 10.1039/c4tb00495g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Quantum dot conjugatedS. cerevisiaeas smart nanotoxicity indicators for screening the toxicity of nanomaterials.
Collapse
Affiliation(s)
- Raghuraj S. Chouhan
- Sabanci University Nanotechnology Research and Application Center
- 34956 Istanbul, Turkey
| | - Anjum Qureshi
- Sabanci University Nanotechnology Research and Application Center
- 34956 Istanbul, Turkey
| | - Javed H. Niazi
- Sabanci University Nanotechnology Research and Application Center
- 34956 Istanbul, Turkey
| |
Collapse
|
26
|
Nagaraja AT, Sooresh A, Meissner KE, McShane MJ. Processing and characterization of stable, pH-sensitive layer-by-layer modified colloidal quantum dots. ACS NANO 2013; 7:6194-6202. [PMID: 23782214 DOI: 10.1021/nn402061t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Quantum Dots (QDs) stabilized with dihydrolipoic acid (DHLA) were used as a template for layer-by-layer (LbL) modification to study the effect on the QD optical properties. We studied several different polyelectrolytes to determine that large quantities of monodisperse DHLA-QDs could only be obtained with the weak polyelectrolyte pair of poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA). The key to this success was the development of a two-step method to split the LbL process into adsorption and centrifugation phases, which require different pH solutions for optimum success. Solution pH is highlighted as an important factor to achieve sufficient QD surface coverage and QD recovery during wash cycles. We optimized the process to scale up synthesis by introducing a solvent precipitation step before ultracentrifugation that, when coupled with the correct pH conditions, results in a mean QD recovery of 86-90% after three wash cycles. We found that adsorption of PAH had a negligible effect on the quantum yield and lifetime but an additional layer of PAA resulted in a substantial decrease in both quantum yield and lifetime that could not be recovered by the addition of more layers. The PAH coating provides a protective coating that extends DHLA-QDs stability, prevents photo-oxidation mediated aggregation, alleviates concerns over batch variability, and results in pH-dependent emission.
Collapse
Affiliation(s)
- Ashvin T Nagaraja
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | | | | | | |
Collapse
|
27
|
Boeneman K, Delehanty JB, Blanco-Canosa JB, Susumu K, Stewart MH, Oh E, Huston AL, Dawson G, Ingale S, Walters R, Domowicz M, Deschamps JR, Algar WR, DiMaggio S, Manono J, Spillmann CM, Thompson D, Jennings TL, Dawson PE, Medintz IL. Selecting improved peptidyl motifs for cytosolic delivery of disparate protein and nanoparticle materials. ACS NANO 2013; 7:3778-96. [PMID: 23710591 PMCID: PMC3880025 DOI: 10.1021/nn400702r] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cell penetrating peptides facilitate efficient intracellular uptake of diverse materials ranging from small contrast agents to larger proteins and nanoparticles. However, a significant impediment remains in the subsequent compartmentalization/endosomal sequestration of most of these cargoes. Previous functional screening suggested that a modular peptide originally designed to deliver palmitoyl-protein thioesterase inhibitors to neurons could mediate endosomal escape in cultured cells. Here, we detail properties relevant to this peptide's ability to mediate cytosolic delivery of quantum dots (QDs) to a wide range of cell-types, brain tissue culture and a developing chick embryo in a remarkably nontoxic manner. The peptide further facilitated efficient endosomal escape of large proteins, dendrimers and other nanoparticle materials. We undertook an iterative structure-activity relationship analysis of the peptide by discretely modifying key components including length, charge, fatty acid content and their order using a comparative, semiquantitative assay. This approach allowed us to define the key motifs required for endosomal escape, to select more efficient escape sequences, along with unexpectedly identifying a sequence modified by one methylene group that specifically targeted QDs to cellular membranes. We interpret our results within a model of peptide function and highlight implications for in vivo labeling and nanoparticle-mediated drug delivery by using different peptides to co-deliver cargoes to cells and engage in multifunctional labeling.
Collapse
Affiliation(s)
- Kelly Boeneman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - James B. Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Juan B. Blanco-Canosa
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Programme, Barcelona 08028 Spain
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- Sotera Defense Solutions, Annapolis Junction, MD 20701 U.S.A
| | - Michael H. Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- Sotera Defense Solutions, Annapolis Junction, MD 20701 U.S.A
| | - Alan L. Huston
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Glyn Dawson
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
| | - Sampat Ingale
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Ryan Walters
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Programme, Barcelona 08028 Spain
| | - Miriam Domowicz
- Departments of Pediatrics, Biochemistry, Committee on Neurobiology, University of Chicago, Chicago, IL 60637 U.S.A
| | - Jeffrey R. Deschamps
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - W. Russ Algar
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
- College of Science, George Mason University, Fairfax, VA 22030 U.S.A
| | - Stassi DiMaggio
- Department of Chemistry, Xavier University of Louisiana, New Orleans LA 70125 U.S.A
| | - Janet Manono
- Department of Chemistry, Xavier University of Louisiana, New Orleans LA 70125 U.S.A
| | - Christopher M. Spillmann
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| | - Darren Thompson
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Travis L. Jennings
- eBioscience, Inc., 10255 Science Center Drive, San Diego, CA 92121 U.S.A
| | - Philip E. Dawson
- Departments of Cell Biology & Chemistry, The Scripps Research Institute, La Jolla, CA 92037 U.S.A
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375 U.S.A
| |
Collapse
|
28
|
Edwards KA, Baeumner AJ. Periplasmic Binding Protein-Based Detection of Maltose Using Liposomes: A New Class of Biorecognition Elements in Competitive Assays. Anal Chem 2013; 85:2770-8. [DOI: 10.1021/ac303258n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Katie A. Edwards
- Cornell University, Department
of Biological and Environmental Engineering, 140 Riley-Robb Hall,
Ithaca, New York 14853, United States
| | - Antje J. Baeumner
- Cornell University, Department
of Biological and Environmental Engineering, 140 Riley-Robb Hall,
Ithaca, New York 14853, United States
| |
Collapse
|
29
|
Boeneman Gemmill K, Deschamps JR, Delehanty JB, Susumu K, Stewart MH, Glaven RH, Anderson GP, Goldman ER, Huston AL, Medintz IL. Optimizing protein coordination to quantum dots with designer peptidyl linkers. Bioconjug Chem 2013; 24:269-81. [PMID: 23379817 DOI: 10.1021/bc300644p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Semiconductor quantum dots (QDs) demonstrate select optical properties that make them of particular use in biological imaging and biosensing. Controlled attachment of biomolecules such as proteins to the QD surface is thus critically necessary for development of these functional nanobiomaterials. QD surface coatings such as poly(ethylene glycol) impart colloidal stability to the QDs, making them usable in physiological environments, but can impede attachment of proteins due to steric interactions. While this problem is being partially addressed through the development of more compact QD ligands, here we present an alternative and complementary approach to this issue by engineering rigid peptidyl linkers that can be appended onto almost all expressed proteins. The linkers are specifically designed to extend a terminal polyhistidine sequence out from the globular protein structure and penetrate the QD ligand coating to enhance binding by metal-affinity driven coordination. α-Helical linkers of two lengths terminating in either a single or triple hexahistidine motif were fused onto a single-domain antibody; these were then self-assembled onto QDs to create a model immunosensor system targeted against the biothreat agent ricin. We utilized this system to systematically evaluate the peptidyl linker design in functional assays using QDs stabilized with four different types of coating ligands including poly(ethylene glycol). We show that increased linker length, but surprisingly not added histidines, can improve protein to QD attachment and sensor performance despite the surface ligand size with both custom and commercial QD preparations. Implications for these findings on the development of QD-based biosensors are discussed.
Collapse
Affiliation(s)
- Kelly Boeneman Gemmill
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Frascione N, Gooch J, Daniel B. Enabling fluorescent biosensors for the forensic identification of body fluids. Analyst 2013; 138:7279-88. [DOI: 10.1039/c3an01372c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
31
|
Chouhan RS, Niazi JH, Qureshi A. E. coli–quantum dot bioconjugates as whole-cell fluorescent reporters for probing cellular damage. J Mater Chem B 2013; 1:2724-2730. [DOI: 10.1039/c3tb20338g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
32
|
Dacres H, Michie M, Anderson A, Trowell SC. Advantages of substituting bioluminescence for fluorescence in a resonance energy transfer-based periplasmic binding protein biosensor. Biosens Bioelectron 2012; 41:459-64. [PMID: 23083905 DOI: 10.1016/j.bios.2012.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 11/26/2022]
Abstract
A genetically encoded maltose biosensor was constructed, comprising maltose binding protein (MBP) flanked by a green fluorescent protein (GFP(2)) at the N-terminus and a Renilla luciferase variant (RLuc2) at the C-terminus. This Bioluminescence resonance energy transfer(2) (BRET(2)) system showed a 30% increase in the BRET ratio upon maltose binding, compared with a 10% increase with an equivalent fluorescence resonance energy transfer (FRET) biosensor. BRET(2) provides a better matched Förster distance to the known separation of the N and C termini of MBP than FRET. The sensor responded to maltose and maltotriose and the response was completely abolished by introduction of a single point mutation in the BRET(2) tagged MBP protein. The half maximal effective concentration (EC(50)) was 0.37 μM for maltose and the response was linear over almost three log units ranging from 10nM to 3.16 μM maltose for the BRET(2) system compared to an EC(50) of 2.3 μM and a linear response ranging from 0.3 μM to 21.1 μM for the equivalent FRET-based biosensor. The biosensor's estimate of maltose in beer matched that of a commercial enzyme-linked assay but was quicker and more precise, demonstrating its applicability to real-world samples. A similar BRET(2)-based transduction scheme approach would likely be applicable to other binding proteins that have a "venus-fly-trap" mechanism.
Collapse
Affiliation(s)
- Helen Dacres
- CSIRO Food Futures National Research Flagship & Ecosystem Sciences, Australia, Canberra ACT 2601, Australia.
| | | | | | | |
Collapse
|
33
|
Long F, Gu C, Gu AZ, Shi H. Quantum Dot/Carrier–Protein/Haptens Conjugate as a Detection Nanobioprobe for FRET-Based Immunoassay of Small Analytes with All-Fiber Microfluidic Biosensing Platform. Anal Chem 2012; 84:3646-53. [DOI: 10.1021/ac3000495] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Feng Long
- State Key Joint
Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, People’s
Republic of China
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
United States
| | - Chunmei Gu
- State Key Joint
Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, People’s
Republic of China
| | - April Z. Gu
- Department of Civil
and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hanchang Shi
- State Key Joint
Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, People’s
Republic of China
| |
Collapse
|
34
|
Chen Q, Wei W, Lin JM. Homogeneous detection of concanavalin A using pyrene-conjugated maltose assembled graphene based on fluorescence resonance energy transfer. Biosens Bioelectron 2011; 26:4497-502. [DOI: 10.1016/j.bios.2011.05.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/21/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
|
35
|
Ziessel R, Harriman A. Artificial light-harvesting antennae: electronic energy transfer by way of molecular funnels. Chem Commun (Camb) 2011; 47:611-31. [DOI: 10.1039/c0cc02687e] [Citation(s) in RCA: 342] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
36
|
Asher WB, Bren KL. A heme fusion tag for protein affinity purification and quantification. Protein Sci 2010; 19:1830-9. [PMID: 20665691 PMCID: PMC2998719 DOI: 10.1002/pro.460] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/07/2010] [Accepted: 07/09/2010] [Indexed: 11/10/2022]
Abstract
We report a novel affinity-based purification method for proteins expressed in Escherichia coli that uses the coordination of a heme tag to an L-histidine-immobilized sepharose (HIS) resin. This approach provides an affinity purification tag visible to the eye, facilitating tracking of the protein. We show that azurin and maltose binding protein are readily purified from cell lysate using the heme tag and HIS resin. Mild conditions are used; heme-tagged proteins are bound to the HIS resin in phosphate buffer, pH 7.0, and eluted by adding 200-500 mM imidazole or binding buffer at pH 5 or 8. The HIS resin exhibits a low level of nonspecific binding of untagged cellular proteins for the systems studied here. An additional advantage of the heme tag-HIS method for purification is that the heme tag can be used for protein quantification by using the pyridine hemochrome absorbance method for heme concentration determination.
Collapse
Affiliation(s)
| | - Kara L Bren
- Department of Chemistry, University of RochesterRochester, New York 14627-0216
| |
Collapse
|
37
|
Prasuhn DE, Deschamps JR, Susumu K, Stewart MH, Boeneman K, Blanco-Canosa JB, Dawson PE, Medintz IL. Polyvalent display and packing of peptides and proteins on semiconductor quantum dots: predicted versus experimental results. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:555-564. [PMID: 20077423 DOI: 10.1002/smll.200901845] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Quantum dots (QDs) are loaded with a series of peptides and proteins of increasing size, including a <20 residue peptide, myoglobin, mCherry, and maltose binding protein, which together cover a range of masses from <2.2 to approximately 44 kDa. Conjugation to the surface of dihydrolipoic acid-functionalized QDs is facilitated by polyhistidine metal affinity coordination. Increasing ratios of dye-labeled peptides and proteins are self-assembled to the QDs and then the bioconjugates are separated and analyzed using agarose gel electrophoresis. Fluorescent visualization of both conjugated and unbound species allows determination of an experimentally derived maximum loading number. Molecular modeling utilizing crystallographic coordinates or space-filling structures of the peptides and proteins also allow the predicted maximum loadings to the QDs to be estimated. Comparison of the two sets of results provides insight into the nature of the QD surface and reflects the important role played by the nanoparticle's hydrophilic solubilizing surface ligands. It is found that for the larger protein molecules steric hindrance is the major packing constraint. In contrast, for the smaller peptides, the number of available QD binding sites is the principal determinant. These results can contribute towards an overall understanding of how to engineer designer bioconjugates for both QDs and other nanoparticle materials.
Collapse
Affiliation(s)
- Duane E Prasuhn
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Dif A, Boulmedais F, Pinot M, Roullier V, Baudy-Floc'h M, Coquelle FM, Clarke S, Neveu P, Vignaux F, Le Borgne R, Dahan M, Gueroui Z, Marchi-Artzner V. Small and stable peptidic PEGylated quantum dots to target polyhistidine-tagged proteins with controlled stoichiometry. J Am Chem Soc 2010; 131:14738-46. [PMID: 19788248 DOI: 10.1021/ja902743u] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The use of the semiconductor quantum dots (QD) as biolabels for both ensemble and single-molecule tracking requires the development of simple and versatile methods to target individual proteins in a controlled manner, ideally in living cells. To address this challenge, we have prepared small and stable QDs (QD-ND) using a surface coating based on a peptide sequence containing a tricysteine, poly(ethylene glycol) (PEG), and an aspartic acid ligand. These QDs, with a hydrodynamic diameter of 9 +/- 1.5 nm, can selectively bind to polyhistidine-tagged (histag) proteins in vitro or in living cells. We show that the small and monodisperse size of QD-ND allows for the formation of QD-ND/histag protein complexes of well-defined stoichiometry and that the 1:1 QD/protein complex can be isolated and purified by gel electrophoresis without any destabilization in the nanomolar concentration range. We also demonstrate that QD-ND can be used to specifically label a membrane receptor with an extracellular histag expressed in living HeLa cells. Here, cytotoxicity tests reveal that cell viability remains high under the conditions required for cellular labeling with QD-ND. Finally, we apply QD-ND complexed with histag end binding protein-1 (EB1), a microtubule associated protein, to single-molecule tracking in Xenopus extracts. Specific colocalization of QD-ND/EB1 with microtubules during the mitotic spindle formation demonstrates that QD-ND and our labeling strategy provide an efficient approach to monitor the dynamic behavior of proteins involved in complex biological functions.
Collapse
Affiliation(s)
- Aurélien Dif
- Université de Rennes 1, CNRS UMR 6226, Sciences Chimiques de Rennes, Rennes, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Wang H, Nakata E, Hamachi I. Recent progress in strategies for the creation of protein-based fluorescent biosensors. Chembiochem 2010; 10:2560-77. [PMID: 19693761 DOI: 10.1002/cbic.200900249] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein-based fluorescent biosensors--integrated devices that convert a molecular-recognition event to a fluorescent signal--have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein-based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.
Collapse
Affiliation(s)
- Hangxiang Wang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | | | | |
Collapse
|
40
|
Patsenker LD, Tatarets AL, Klochko OP, Terpetschnig EA. Conjugates, Complexes, and Interlocked Systems Based on Squaraines and Cyanines. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY II 2010. [DOI: 10.1007/978-3-642-04701-5_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
41
|
Slade KM, Baker R, Chua M, Thompson NL, Pielak GJ. Effects of recombinant protein expression on green fluorescent protein diffusion in Escherichia coli. Biochemistry 2009; 48:5083-9. [PMID: 19413350 DOI: 10.1021/bi9004107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence recovery after photobleaching was used to measure the diffusion coefficient of green fluorescent protein (GFP, 27 kDa) in Escherichia coli in the presence or absence of four coexpressed proteins: cytoplasmic maltose binding protein (42 kDa), tau-40 (45 kDa), alpha-synuclein (14 kDa), or calmodulin (17 kDa). The GFP diffusion coefficient remains constant regardless of the type of coexpresseed protein and whether or not the coexpressed protein was induced. We conclude that expression of these soluble proteins has little to no effect on the diffusion of GFP. These results have implications for the utility of in-cell nuclear magnetic resonance spectroscopy.
Collapse
Affiliation(s)
- Kristin M Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | | | | | | | | |
Collapse
|
42
|
Yakovlev AV, Zhang F, Zulqurnain A, Azhar-Zahoor A, Luccardini C, Gaillard S, Mallet JM, Tauc P, Brochon JC, Parak WJ, Feltz A, Oheim M. Wrapping nanocrystals with an amphiphilic polymer preloaded with fixed amounts of fluorophore generates FRET-based nanoprobes with a controlled donor/acceptor ratio. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3232-9. [PMID: 19437725 DOI: 10.1021/la8038347] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Colloidal nanocrystal (NC) donors wrapped with a polymer coating including multiple organic acceptor molecules are promising scaffolds for fluorescence resonance energy transfer (FRET)-based nanobiosensors. Over other self-assembling donor-acceptor configurations, our preloaded polymers have the virtue of producing compact assemblies with a fixed donor/acceptor distance. This property, together with the possibility of stoichiometric polymer loading, allowed us to directly address how the FRET efficiency depended on the donor/acceptor. At the population level, nanoprobes based on commercial as well as custom CdSe/ZnS donors displayed the expected dose-dependent rise in transfer efficiency, saturating from about five ATTO dyes/NC. However, for a given acceptor concentration, both the intensity and lifetime of single-pair FRET data revealed a large dispersion of transfer efficiencies, highlighting an important heterogeneity among nominally identical FRET-based nanoprobes. Rigorous quality check during synthesis and shell assembly as well as postsynthesis sorting and purification are required to make hybrid semiconductor-organic nanoprobes a robust and viable alternative to organic or genetically encoded nanobiosensors.
Collapse
|
43
|
Medintz IL, Pons T, Delehanty JB, Susumu K, Brunel FM, Dawson PE, Mattoussi H. Intracellular delivery of quantum dot-protein cargos mediated by cell penetrating peptides. Bioconjug Chem 2008; 19:1785-95. [PMID: 18681468 DOI: 10.1021/bc800089r] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We utilize cell penetrating peptide functionalized QDs as specific vectors for the intracellular delivery of model fluorescent protein cargos. Multiple copies of two structurally diverse fluorescent proteins, the 27 kDa monomeric yellow fluorescent protein and the 240 kDa multichromophore b-phycoerythrin complex, were attached to QDs using either metal-affinity driven self-assembly or biotin-Streptavidin binding, respectively. Cellular uptake of these complexes was found to depend on the additional presence of cell-penetrating peptides within the QD-protein conjugates. Once inside the cells, the QD conjugates were mostly distributed within endolysosomal compartments, indicating that intracellular delivery of both QD assemblies was primarily driven by endocytotic uptake. Cellular microinjection of QD-fluorescent protein assemblies was also utilized as an alternate delivery strategy that could bypass the endocytic pathway. Simultaneous signals from both the QDs and the fluorescent proteins allowed verification of their colocalization and conjugate integrity upon delivery inside live cells. Due to their intrinsic fluorescence properties, this class of proteins provides a unique tool to test the ability of QDs functionalized with cell penetrating peptides to mediate the intracellular delivery of both small and large size protein cargos. Use of QD-peptide/fluorescent protein vectors may make powerful tools for understanding the mechanisms of nanoparticle-mediated drug delivery.
Collapse
Affiliation(s)
- Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | | | | | | | | | | | | |
Collapse
|
44
|
Koshi Y, Nakata E, Yamane H, Hamachi I. A fluorescent lectin array using supramolecular hydrogel for simple detection and pattern profiling for various glycoconjugates. J Am Chem Soc 2007; 128:10413-22. [PMID: 16895406 DOI: 10.1021/ja0613963] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because sugar and its derivatives play important roles in various biological phenomena, the rapid and high-throughput analysis of various glycoconjugates is keenly desirable. We describe herein the construction of a novel fluorescent lectin array for saccharide detection using a supramolecular hydrogel matrix. In this array, the fluorescent lectins were noncovalently fixed under semi-wet conditions to suppress the protein denaturation. It is demonstrated by fluorescence titration and fluorescence lifetime experiments that the immobilized lectins act as a molecular recognition scaffold in the hydrogel matrix, similar to that in aqueous solution. That is, a bimolecular fluorescence quenching and recovery (BFQR) method can successfully operate under both conditions. This enables one to fluorescently read-out a series of saccharides on the basis of the recognition selectivity and affinity of the immobilized lectins without tedious washing processes and without labeling the target saccharides. Simple and high-throughput sensing and profiling were carried out using the present lectin array for diverse glycoconjugates, which not only included a simple glucose, but also oligosaccharides, and glycoproteins, and, furthermore, the pattern recognition and profiling of several types of cell lysates were also accomplished.
Collapse
Affiliation(s)
- Yoichiro Koshi
- PRESTO (Synthesis and Control, JST), Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | | | | | | |
Collapse
|
45
|
Emrich CA, Medintz IL, Chu WK, Mathies RA. Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling. Anal Chem 2007; 79:7360-6. [PMID: 17822308 DOI: 10.1021/ac0711485] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microfluidic separation system is developed to perform two-dimensional differential gel electrophoretic (DIGE) separations of complex, cellular protein mixtures produced by induced protein expression in E. coli. The micro-DIGE analyzer is a two-layer borosilicate glass microdevice consisting of a single 3.75 cm long channel for isoelectric focusing, which is sampled in parallel by 20 channels effecting a second-dimension separation by native electrophoresis. The connection between the orthogonal separation systems is accomplished by smaller channels comprising a microfluidic interface (MFI) that prevents media leakage between the two dimensions and enables facile loading of discontinuous gel systems in each dimension. Proteins are covalently labeled with Cy2 and Cy3 DIGE and detected simultaneously with a rotary confocal fluorescence scanner. Reproducible two-dimensional separations of both purified proteins and complex protein mixtures are performed with minimal run-to-run variation by including 7 M urea in the second-dimension separation matrix. The capabilities of the micro-DIGE analyzer are demonstrated by following the induced expression of maltose binding protein in E. coli. Although the absence of sodium dodecyl sulfate (SDS) in the second-dimension sizing separation limits the orthogonality and peak capacity of the separation, this analyzer is a significant first step toward the reproducible two-dimensional analysis of complex protein samples in microfabricated devices. Furthermore, the microchannel interface structures developed here will facilitate other multidimensional separations in microdevices.
Collapse
Affiliation(s)
- Charles A Emrich
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
| | | | | | | |
Collapse
|
46
|
Medintz IL, Sapsford KE, Clapp AR, Pons T, Higashiya S, Welch JT, Mattoussi H. Designer variable repeat length polypeptides as scaffolds for surface immobilization of quantum dots. J Phys Chem B 2007; 110:10683-90. [PMID: 16771314 DOI: 10.1021/jp060611z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the use of a series of engineered, variable-length de novo polypeptides to discretely immobilize luminescent semiconductor nanocrystals or quantum dots (QDs) onto functional surfaces. The polypeptides express N-terminal dicysteine and C-terminal hexahistidine residues that flank a variable number (1, 3, 5, 7, 14, 21, 28, or 35) of core beta-strand repeats, with tyrosine, glutamic acid, histidine, and lysine residues located at the turns. Polypeptides have molecular weights ranging from 4 to 83 kDa and retain a rigid structure based on the antiparallel beta-sheet motif. We first use a series of dye-labeled polypeptides to test and characterize their self-assembly onto hydrophilic CdSe-ZnS QDs using fluorescence resonance energy transfer (FRET). Results indicate that peptides maintain their beta-sheet conformation after self-assembly onto the QD surfaces, regardless of their length. We then immobilize biotinylated derivatives of these polypeptides on a NeutrAvidin-functionalized substrate and use them to capture QDs via specific interactions between the peptides' polyhistidine residues and the nanocrystal surface. We found that each of the polypeptides was able to efficiently capture QDs, with a clear correlation between the density of the surface-tethered peptide and the capacity for nanocrystal capture. The versatility of this capture strategy is highlighted by the creation of a variety of one- and two-dimensional polypeptide-QD structures as well as a self-assembled surface-immobilized FRET-based nutrient sensor.
Collapse
Affiliation(s)
- Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | | | | | | | | | | | | |
Collapse
|
47
|
Liang S, Pierce DT, Amiot C, Zhao X. Photoactive Nanomaterials for Sensing Trace Analytes in Biological Samples. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/15533170500299859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Song Liang
- a Department of Chemistry , University of North Dakota , Grand Forks, North Dakota, USA
| | - David T. Pierce
- a Department of Chemistry , University of North Dakota , Grand Forks, North Dakota, USA
| | - Carrie Amiot
- a Department of Chemistry , University of North Dakota , Grand Forks, North Dakota, USA
| | - Xaiojun Zhao
- a Department of Chemistry , University of North Dakota , Grand Forks, North Dakota, USA
| |
Collapse
|
48
|
Pons T, Medintz IL, Wang X, English DS, Mattoussi H. Solution-Phase Single Quantum Dot Fluorescence Resonance Energy Transfer. J Am Chem Soc 2006; 128:15324-31. [PMID: 17117885 DOI: 10.1021/ja0657253] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a single particle fluorescence resonance energy transfer (spFRET) study of freely diffusing self-assembled quantum dot (QD) bioconjugate sensors, composed of CdSe-ZnS core-shell QD donors surrounded by dye-labeled protein acceptors. We first show that there is direct correlation between single particle and ensemble FRET measurements in terms of derived FRET efficiencies and donor-acceptor separation distances. We also find that, in addition to increased sensitivity, spFRET provides information about FRET efficiency distributions which can be used to resolve distinct sensor subpopulations. We use this capacity to gain information about the distribution in the valence of self-assembled QD-protein conjugates and show that this distribution follows Poisson statistics. We then apply spFRET to characterize heterogeneity in single sensor interactions with the substrate/target and show that such heterogeneity varies with the target concentration. The binding constant derived from spFRET is consistent with ensemble measurements.
Collapse
Affiliation(s)
- Thomas Pons
- Optical Sciences Division, Code 5611, Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, Washington, D.C. 20375, USA
| | | | | | | | | |
Collapse
|
49
|
Pons T, Uyeda HT, Medintz IL, Mattoussi H. Hydrodynamic Dimensions, Electrophoretic Mobility, and Stability of Hydrophilic Quantum Dots. J Phys Chem B 2006; 110:20308-16. [PMID: 17034212 DOI: 10.1021/jp065041h] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Luminescent semiconductor quantum dots (QDs) have great potential for use in biological assays and imaging. These nanocrystals are capped with surface ligands (bifunctional molecules, amphiphilic polymers, phospholipids, etc.) that render them hydrophilic and provide them with functional properties. These coatings alters their hydrodynamic radii and surface charge, which can drastically affect properties such as diffusion within the cell cytoplasm. Heavy atom techniques such as transmission electron microscopy and X-ray scattering probe the inorganic core and do not take into account the ligand coating. Herein we use dynamic light scattering to characterize the hydrodynamic radius (R(H)) of CdSe-ZnS QDs capped with various hydrophilic surface coatings (including dihydrolipoic acid and amphiphilic polymers) and self-assembled QD-protein bioconjugates. Experiments were complemented with measurements of the geometric size and zeta potential using agarose gel electrophoresis and laser Doppler velocimetry. We find that the effects of surface ligands on the hydrodynamic radius and on the nanoparticle mobility are complex and strongly depend on a combination of the inorganic core size and nature and lateral extension of the hydrophilic surface coating. These properties are critical for the design of QD-based biosensing assays as well as QD bioconjugate diffusion in live cells.
Collapse
Affiliation(s)
- Thomas Pons
- Optical Sciences Division and Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | | | | | | |
Collapse
|
50
|
|