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Zhang Y, Min C, Dou X, Wang X, Urbach HP, Somekh MG, Yuan X. Plasmonic tweezers: for nanoscale optical trapping and beyond. LIGHT, SCIENCE & APPLICATIONS 2021; 10:59. [PMID: 33731693 PMCID: PMC7969631 DOI: 10.1038/s41377-021-00474-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/24/2020] [Accepted: 01/14/2021] [Indexed: 05/06/2023]
Abstract
Optical tweezers and associated manipulation tools in the far field have had a major impact on scientific and engineering research by offering precise manipulation of small objects. More recently, the possibility of performing manipulation with surface plasmons has opened opportunities not feasible with conventional far-field optical methods. The use of surface plasmon techniques enables excitation of hotspots much smaller than the free-space wavelength; with this confinement, the plasmonic field facilitates trapping of various nanostructures and materials with higher precision. The successful manipulation of small particles has fostered numerous and expanding applications. In this paper, we review the principles of and developments in plasmonic tweezers techniques, including both nanostructure-assisted platforms and structureless systems. Construction methods and evaluation criteria of the techniques are presented, aiming to provide a guide for the design and optimization of the systems. The most common novel applications of plasmonic tweezers, namely, sorting and transport, sensing and imaging, and especially those in a biological context, are critically discussed. Finally, we consider the future of the development and new potential applications of this technique and discuss prospects for its impact on science.
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Affiliation(s)
- Yuquan Zhang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Changjun Min
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
| | - Xiujie Dou
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Xianyou Wang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Hendrik Paul Urbach
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Michael G Somekh
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xiaocong Yuan
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
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Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Comput Struct Biotechnol J 2020; 18:1577-1586. [PMID: 32637054 PMCID: PMC7330491 DOI: 10.1016/j.csbj.2020.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
Despite the wealth of methods developed for exploring the molecular basis of allostery in biomolecular systems, there is still a need for structure-based predictive tools that can efficiently detect susceptible sites for triggering allosteric responses. Toward this goal, we introduce here an elastic network model (ENM)-based method, Essential Site Scanning Analysis (ESSA). Essential sites are here defined as residues that would significantly alter the protein's global dynamics if bound to a ligand. To mimic the crowding induced upon substrate binding, the heavy atoms of each residue are incorporated as additional network nodes into the α-carbon-based ENM, and the resulting shifts in soft mode frequencies are used as a metric for evaluating the essentiality of each residue. Results on a dataset of monomeric proteins indicate the enrichment of allosteric and orthosteric binding sites, as well as global hinge regions among essential residues, highlighting the significant role of these sites in controlling the overall structural dynamics. Further integration of ESSA with information on predicted pockets and their local hydrophobicity density enables successful predictions of allosteric pockets for both ligand-bound and -unbound structures. ESSA can be efficiently applied to large multimeric systems. Three case studies, namely (i) G-protein binding to a GPCR, (ii) heterotrimeric assembly of the Ser/Thr protein phosphatase PP2A, and (iii) allo-targeting of AMPA receptor, demonstrate the utility of ESSA for identifying essential sites and narrowing down target allosteric sites identified by druggability simulations.
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Frustaci S, Vollmer F. Whispering-gallery mode (WGM) sensors: review of established and WGM-based techniques to study protein conformational dynamics. Curr Opin Chem Biol 2019; 51:66-73. [PMID: 31202140 DOI: 10.1016/j.cbpa.2019.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
Abstract
Monitoring the conformational dynamics of proteins is crucial for a better understanding of their biological functions. To observe the structural dynamics of proteins, it is often necessary to study each molecule individually. To this end, single-molecule techniques have been developed such as Förster resonance energy transfer and optical tweezers. However, although powerful, these techniques do have their limitations, for example, limited temporal resolution, or necessity for fluorescent labelling, and they can often only access a limited set of all protein motions. Here, within the context of established structural biology techniques, we review a new class of highly sensitive optical devices based on WGM, which characterise protein dynamics on previously inaccessible timescales, visualise motions throughout a protein, and track movements of single atoms.
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Affiliation(s)
- Simona Frustaci
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, UK.
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, EX4 4QD, UK.
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Subramanian S, Wu HY, Constant T, Xavier J, Vollmer F. Label-Free Optical Single-Molecule Micro- and Nanosensors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1801246. [PMID: 30073717 DOI: 10.1002/adma.201801246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/23/2018] [Indexed: 05/12/2023]
Abstract
Label-free optical sensor systems have emerged that exhibit extraordinary sensitivity for detecting physical, chemical, and biological entities at the micro/nanoscale. Particularly exciting is the detection and analysis of molecules, on miniature optical devices that have many possible applications in health, environment, and security. These micro- and nanosensors have now reached a sensitivity level that allows for the detection and analysis of even single molecules. Their small size enables an exceedingly high sensitivity, and the application of quantum optical measurement techniques can allow the classical limits of detection to be approached or surpassed. The new class of label-free micro- and nanosensors allows dynamic processes at the single-molecule level to be observed directly with light. By virtue of their small interaction length, these micro- and nanosensors probe light-matter interactions over a dynamic range often inaccessible by other optical techniques. For researchers entering this rapidly advancing field of single-molecule micro- and nanosensors, there is an urgent need for a timely review that covers the most recent developments and that identifies the most exciting opportunities. The focus here is to provide a summary of the recent techniques that have either demonstrated label-free single-molecule detection or claim single-molecule sensitivity.
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Affiliation(s)
- Sivaraman Subramanian
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Hsin-Yu Wu
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Tom Constant
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Jolly Xavier
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Frank Vollmer
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
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Hacohen N, Ip CJX, Gordon R. Analysis of Egg White Protein Composition with Double Nanohole Optical Tweezers. ACS OMEGA 2018; 3:5266-5272. [PMID: 31458737 PMCID: PMC6641915 DOI: 10.1021/acsomega.8b00651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 05/21/2023]
Abstract
We use a double nanohole optical tweezer to analyze the protein composition of egg white through analysis of many individual protein trapping events. The proteins are grouped by mass based on two metrics: standard deviation of the trapping laser intensity fluctuations from the protein diffusion and the time constant of these fluctuations coming from the autocorrelation. Quantitative analysis is demonstrated for artificial samples, and then, the approach is applied to real egg white. The composition found from real egg white corresponds well to past reports using gel electrophoresis. This approach differs from past works by allowing for individual protein analysis in heterogeneous solutions without the need for denaturing, labeling, or tethering.
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Affiliation(s)
- Noa Hacohen
- Faculty of Engineering, Department of Electrical and Computer Engineering, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Candice J X Ip
- Faculty of Engineering, Department of Electrical and Computer Engineering, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Reuven Gordon
- Faculty of Engineering, Department of Electrical and Computer Engineering, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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Nicolaï A, Delarue P, Senet P. Theoretical Insights into Sub-Terahertz Acoustic Vibrations of Proteins Measured in Single-Molecule Experiments. J Phys Chem Lett 2016; 7:5128-5136. [PMID: 27973880 DOI: 10.1021/acs.jpclett.6b01812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteins are an important class of nanobioparticles with acoustical modes in the sub-THz frequency range. There is considerable interest to measure and establish the role of these acoustical vibrations for biological function. So far, the technique providing the most detailed information about the acoustical modes of proteins is the very recent Extraordinary Acoustic Raman (EAR) spectroscopy. In this technique, proteins are trapped in nanoholes and excited by two optical lasers of slightly different wavelengths producing an electric field at low frequency (<100 GHz). We demonstrate that the acoustical modes of proteins studied by EAR spectroscopy are both infrared- and Raman-active modes, and we provided interpretation of the spectroscopic fingerprints measured at the single-molecule level. A combination of the present calculations with techniques based on the excitation of a single nanobioparticle by an electric field, such as EAR spectroscopy, should provide a wealth of information on the role of molecular dynamics for biological function.
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Affiliation(s)
- Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
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