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Sobczak K, Turczyniak-Surdacka S, Lewandowski W, Baginski M, Tupikowska M, González-Rubio G, Wójcik M, Carlsson A, Donten M. STEM Tomography of Au Helical Assemblies. Microsc Microanal 2021; 28:1-5. [PMID: 34169809 DOI: 10.1017/s1431927621012009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Composite, helical nanostructures formed using cooperative interactions of liquid crystals and Au nanoparticles were studied using a scanning transmission electron microscopy (STEM) mode. The investigated helical assemblies exhibit long-range hierarchical order across length scales, as a result of the crystallization (freezing) directed growth mechanism of nanoparticle-coated twisted nanoribbons and their ability to form organized bundles. Here, STEM methods were used to reproduce the 3D structure of the Au nanoparticle double helix.
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Affiliation(s)
- Kamil Sobczak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089Warsaw, Poland
| | - Sylwia Turczyniak-Surdacka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089Warsaw, Poland
| | - Wiktor Lewandowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093Warsaw, Poland
| | - Maciej Baginski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093Warsaw, Poland
| | - Martyna Tupikowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093Warsaw, Poland
| | | | - Michał Wójcik
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093Warsaw, Poland
| | - Anna Carlsson
- Thermo Fisher Scientific, Materials & Structural Analysis, Eindhoven, The Netherlands
| | - Mikołaj Donten
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093Warsaw, Poland
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Szustakiewicz P, Kowalska N, Grzelak D, Narushima T, Góra M, Bagiński M, Pociecha D, Okamoto H, Liz-Marzán LM, Lewandowski W. Supramolecular Chirality Synchronization in Thin Films of Plasmonic Nanocomposites. ACS Nano 2020; 14:12918-12928. [PMID: 32886482 PMCID: PMC7596782 DOI: 10.1021/acsnano.0c03964] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mirror symmetry breaking in materials is a fascinating phenomenon that has practical implications for various optoelectronic technologies. Chiral plasmonic materials are particularly appealing due to their strong and specific interactions with light. In this work we broaden the portfolio of available strategies toward the preparation of chiral plasmonic assemblies, by applying the principles of chirality synchronization-a phenomenon known for small molecules, which results in the formation of chiral domains from transiently chiral molecules. We report the controlled cocrystallization of 23 nm gold nanoparticles and liquid crystal molecules yielding domains made of highly ordered, helical nanofibers, preferentially twisted to the right or to the left within each domain. We confirmed that such micrometer sized domains exhibit strong, far-field circular dichroism (CD) signals, even though the bulk material is racemic. We further highlight the potential of the proposed approach to realize chiral plasmonic thin films by using a mechanical chirality discrimination method. Toward this end, we developed a rapid CD imaging technique based on the use of polarized light optical microscopy (POM), which enabled probing the CD signal with micrometer-scale resolution, despite of linear dichroism and birefringence in the sample. The developed methodology allows us to extend intrinsically local effects of chiral synchronization to the macroscopic scale, thereby broadening the available tools for chirality manipulation in chiral plasmonic systems.
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Affiliation(s)
- Piotr Szustakiewicz
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Natalia Kowalska
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Dorota Grzelak
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Tetsuya Narushima
- Institute
for Molecular Science (IMS) and The Graduate University for Advanced
Studies (SOKENDAI), 38
Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Monika Góra
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Maciej Bagiński
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Damian Pociecha
- Faculty
of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warsaw, Poland
| | - Hiromi Okamoto
- Institute
for Molecular Science (IMS) and The Graduate University for Advanced
Studies (SOKENDAI), 38
Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Luis M. Liz-Marzán
- CIC
biomaGUNE, Basque Research and Technology
Alliance (BRTA), Paseo
de Miramón 182, Donostia-San Sebastián 20014, Spain
- Ikerbasque,
Basque Foundation for Science, 48013 Bilbao, Spain
- Centro
de Investigación en Biomédica Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramón 182, Donostia-San Sebastián 20014, Spain
| | - Wiktor Lewandowski
- Laboratory
of Organic Nanomaterials and Biomolecules, Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
- (W.L.)
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Zheng W, Pena A, Low WW, Wong JLC, Frankel G, Egelman EH. Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae. Structure 2020; 28:1321-1328.e2. [PMID: 32916103 DOI: 10.1016/j.str.2020.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 01/19/2023]
Abstract
Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism in the spread of antibiotic resistance. Filamentous bacteriophages have been shown to exist in two different structural classes: those with a 5-fold rotational symmetry and those with a one-start helix with approximately 5 subunits per turn. Structures for the F and the F-like pED208 conjugation pilus have shown that they have 5-fold rotational symmetry. Here, we report the cryoelectron-microscopic structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae, encoded on the IncFIIK pKpQIL plasmid, at 3.9 Å resolution and show that it has a one-start helix. These results establish that conjugation pili can exist in at least two structural classes, consistent with other results showing that relatively small perturbations are needed to change the helical symmetry of polymers.
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Affiliation(s)
- Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Alejandro Pena
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Wen Wen Low
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Joshua L C Wong
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Gad Frankel
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
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Debs GE, Cha M, Liu X, Huehn AR, Sindelar CV. Dynamic and asymmetric fluctuations in the microtubule wall captured by high-resolution cryoelectron microscopy. Proc Natl Acad Sci U S A 2020; 117:16976-84. [PMID: 32636254 DOI: 10.1073/pnas.2001546117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microtubules are tubular polymers with essential roles in numerous cellular activities. Structures of microtubules have been captured at increasing resolution by cryo-EM. However, dynamic properties of the microtubule are key to its function, and this behavior has proved difficult to characterize at a structural level due to limitations in existing structure determination methods. We developed a high-resolution cryo-EM refinement method that divides an imaged microtubule into its constituent protofilaments, enabling deviations from helicity and other sources of heterogeneity to be quantified and corrected for at the single-subunit level. We demonstrate that this method improves the resolution of microtubule 3D reconstructions and substantially reduces anisotropic blurring artifacts, compared with methods that utilize helical symmetry averaging. Moreover, we identified an unexpected, discrete behavior of the m-loop, which mediates lateral interactions between neighboring protofilaments and acts as a flexible hinge between them. The hinge angle adopts preferred values corresponding to distinct conformations of the m-loop that are incompatible with helical symmetry. These hinge angles fluctuate in a stochastic manner, and perfectly cylindrical microtubule conformations are thus energetically and entropically penalized. The hinge angle can diverge further from helical symmetry at the microtubule seam, generating a subpopulation of highly distorted microtubules. However, the seam-distorted subpopulation disappears in the presence of Taxol, a microtubule stabilizing agent. These observations provide clues into the structural origins of microtubule flexibility and dynamics and highlight the role of structural polymorphism in defining microtubule behavior.
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Padhi S, Ramakrishna S, Priyakumar UD. Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach. J Comput Chem 2015; 36:539-52. [PMID: 25565454 DOI: 10.1002/jcc.23828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 11/12/2022]
Abstract
An understanding of structure-function relationships of membrane proteins continues to be a challenging problem, owing to the difficulty in obtaining their structures experimentally. This study suggests a method for modeling membrane protein structures that can be used to generate a reliable initial conformation prior to the use of other approaches for sampling conformations. It involves optimizing the orientation of hydrophilic residues so as to minimize unfavorable contacts with the hydrophobic tails of the lipid bilayer. Starting with the optimized initial conformation for three different proteins modeled based on this method, two independent approaches have been used for sampling the conformational space of the proteins. Both approaches are able to predict structures reasonably close to experimental structures, indicating that the initial structure enables the sampling of conformations that are close to the native structure. Possible improvements in the method for making it broadly applicable to helical membrane proteins are discussed.
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Affiliation(s)
- Siladitya Padhi
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
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