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Kim C, Kim Y, Lee SJ, Yun SR, Choi J, Kim SO, Yang Y, Ihee H. Visualizing Heterogeneous Protein Conformations with Multi-Tilt Nanoparticle-Aided Cryo-Electron Microscopy Sampling. NANO LETTERS 2023; 23:3334-3343. [PMID: 37068052 PMCID: PMC10141564 DOI: 10.1021/acs.nanolett.3c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Obtaining the heterogeneous conformation of small proteins is important for understanding their biological role, but it is still challenging. Here, we developed a multi-tilt nanoparticle-aided cryo-electron microscopy sampling (MT-NACS) technique that enables the observation of heterogeneous conformations of small proteins and applied it to calmodulin. By imaging the proteins labeled by two gold nanoparticles at multiple tilt angles and analyzing the projected positions of the nanoparticles, the distributions of 3D interparticle distances were obtained. From the measured distance distributions, the conformational changes associated with Ca2+ binding and salt concentration were determined. MT-NACS was also used to track the structural change accompanied by the interaction between amyloid-beta and calmodulin, which has never been observed experimentally. This work offers an alternative platform for studying the functional flexibility of small proteins.
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Affiliation(s)
- Changin Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yeeun Kim
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
| | - Sang Jin Lee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yongsoo Yang
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Y.Y.:
email, ; tel, +82-42-350-7303
| | - Hyotcherl Ihee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
- H.I.: email, ; tel, +82-42-350-2844
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Obstarczyk P, Pniakowska A, Nonappa, Grzelczak MP, Olesiak-Bańska J. Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging. ACS OMEGA 2023; 8:11503-11511. [PMID: 37008092 PMCID: PMC10061685 DOI: 10.1021/acsomega.3c00426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 12/01/2023]
Abstract
The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.
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Affiliation(s)
- Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Anna Pniakowska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Nonappa
- Faculty
of Engineering and Natural Sciences, Tampere
University, FI-33720 Tampere, Finland
| | - Marcin P. Grzelczak
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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