1
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Kumashiro M, Matsuo K. Characterization of membrane-interaction mechanisms of proteins using vacuum-ultraviolet circular dichroism spectroscopy. Chirality 2023; 35:826-837. [PMID: 37418251 DOI: 10.1002/chir.23607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Protein-membrane interactions play an important role in various biological phenomena, such as material transport, demyelinating diseases, and antimicrobial activity. We combined vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy with theoretical (e.g., molecular dynamics and neural networks) and polarization experimental (e.g., linear dichroism and fluorescence anisotropy) methods to characterize the membrane interaction mechanisms of three soluble proteins (or peptides). α1 -Acid glycoprotein has the drug-binding ability, but the combination of VUVCD and neural-network method revealed that the membrane interaction causes the extension of helix in the N-terminal region, which reduces the binding ability. Myelin basic protein (MBP) is an essential component of the myelin sheath with a multi-layered structure. Molecular dynamics simulations using a VUVCD-guided system showed that MBP forms two amphiphilic and three non-amphiphilic helices as membrane interaction sites. These multivalent interactions may allow MBP to interact with two opposing membrane leaflets, contributing to the formation of a multi-layered myelin structure. The antimicrobial peptide magainin 2 interacts with the bacterial membrane, causing damage to its structure. VUVCD analysis revealed that the M2 peptides assemble in the membrane and turn into oligomers with a β-strand structure. Linear dichroism and fluorescence anisotropy suggested that the oligomers are inserted into the hydrophobic core of the membrane, disrupting the bacterial membrane. Overall, our findings demonstrate that VUVCD and its combination with theoretical and polarization experimental methods pave the way for unraveling the molecular mechanisms of biological phenomena related to protein-membrane interactions.
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Affiliation(s)
- Munehiro Kumashiro
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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2
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Formation of β-Strand Oligomers of Antimicrobial Peptide Magainin 2 Contributes to Disruption of Phospholipid Membrane. MEMBRANES 2022; 12:membranes12020131. [PMID: 35207051 PMCID: PMC8877076 DOI: 10.3390/membranes12020131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
The antimicrobial peptide magainin 2 (M2) interacts with and induces structural damage in bacterial cell membranes. Although extensive biophysical studies have revealed the interaction mechanism between M2 and membranes, the mechanism of membrane-mediated oligomerization of M2 is controversial. Here, we measured the synchrotron-radiation circular dichroism and linear dichroism (LD) spectra of M2 in dipalmitoyl-phosphatidylglycerol lipid membranes in lipid-to-peptide (L/P) molar ratios from 0–26 to characterize the conformation and orientation of M2 on the membrane. The results showed that M2 changed from random coil to α-helix structures via an intermediate state with increasing L/P ratio. Singular value decomposition analysis supported the presence of the intermediate state, and global fitting analysis revealed that M2 monomers with an α-helix structure assembled and transformed into M2 oligomers with a β-strand-rich structure in the intermediate state. In addition, LD spectra showed the presence of β-strand structures in the intermediate state, disclosing their orientations on the membrane surface. Furthermore, fluorescence spectroscopy showed that the formation of β-strand oligomers destabilized the membrane structure and induced the leakage of calcein molecules entrapped in the membrane. These results suggest that the formation of β-strand oligomers of M2 plays a crucial role in the disruption of the cell membrane.
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3
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Carter JG, Pfukwa R, Riley L, Tucker JHR, Rodger A, Dafforn TR, Klumperman B. Linear Dichroism Activity of Chiral Poly( p-Aryltriazole) Foldamers. ACS OMEGA 2021; 6:33231-33237. [PMID: 34901675 PMCID: PMC8656205 DOI: 10.1021/acsomega.1c06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 05/04/2023]
Abstract
Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.
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Affiliation(s)
- Jake G. Carter
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Rueben Pfukwa
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
| | - Liam Riley
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Bert Klumperman
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
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4
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Looijmans SFSP, Carmeli E, Puskar L, Ellis G, Cavallo D, Anderson PD, Breemen LCA. Polarization modulated infrared spectroscopy: A pragmatic tool for polymer science and engineering. POLYMER CRYSTALLIZATION 2020. [DOI: 10.1002/pcr2.10138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Stan F. S. P. Looijmans
- Polymer Technology, Department of Mechanical Engineering Eindhoven University of Technology Eindhoven The Netherlands
- DPI Eindhoven The Netherlands
| | - Enrico Carmeli
- Department of Chemistry and Industrial Chemistry University of Genova Genova Italy
| | - Ljiljana Puskar
- Helmholtz‐Zentrum für Materialien und Energie GmbH Albert‐Einstein‐Straße 15 Berlin Germany
| | - Gary Ellis
- Institute of Polymer Science and Technology (ICTP/CSIC) Calle de Juan de la Cierva 3 Madrid Spain
| | - Dario Cavallo
- Department of Chemistry and Industrial Chemistry University of Genova Genova Italy
| | - Patrick D. Anderson
- Polymer Technology, Department of Mechanical Engineering Eindhoven University of Technology Eindhoven The Netherlands
| | - Lambèrt C. A. Breemen
- Polymer Technology, Department of Mechanical Engineering Eindhoven University of Technology Eindhoven The Netherlands
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5
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Masnikosa R, Milutinović MM, Crnolatac I, Tot A, Veličković S, Bojić-Trbojević Ž, Rilak-Simović A. Anti-adhesive action of novel ruthenium(II) chlorophenyl terpyridine complexes with a high affinity for double-stranded DNA: in vitro and in silico. J Inorg Biochem 2020; 208:111090. [PMID: 32389890 DOI: 10.1016/j.jinorgbio.2020.111090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/19/2020] [Accepted: 04/19/2020] [Indexed: 12/01/2022]
Abstract
Interactions of three Ru(II) chlorophenyl terpyridine complexes: [Ru(Cl-Ph-tpy)(en)Cl]Cl (1), [Ru(Cl-Ph-tpy)(dach)Cl]Cl (2) and [Ru(Cl-Ph-tpy)(bpy)Cl]Cl (3) (Cl-Ph-tpy = 4'-(4-chlorophenyl)-2,2':6',2''-terpyridine, en = 1,2-diaminoethane, dach = 1,2-diaminocyclohexane, bpy = 2,2'-bipyridine) with human serum albumin (HSA), calf thymus DNA and a double-helical oligonucleotide d(CGCGAATTCGCG)2 (1BNA) were examined. Fluorescence emission studies were used to assess the interactions of complexes with HSA, which were of moderate strength for 1 and 2. Molecular docking allowed us to predict mostly π-π stacking and van der Waals interactions between the complexes and the protein. We suggest that the complexes bind to a novel site on HSA, which is different from its druggable sites I, II or III. We suggest a partial intercalation of complexes through the minor groove as a possible mode of interaction with double-helical DNA. Finally, when applied to normal extravillous cell line HTR8/SVneo and JAr choriocarcinoma cell line, complexes 1 and 2 exerted anti-adhesive properties at very low doses, whereas complex 3 had a negligible effect. The obtained results are completion of our studies of Ru(II) terpyridyl complexes that carry N-N ancillary ligands. We suggest a new research direction towards studying the cellular effects of Ru(II) polypyridyl compounds.
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Affiliation(s)
- Romana Masnikosa
- Department of Physical Chemistry, Vinca Institute of Nuclear Sciences, University of Belgrade, Mike Petrovića Alasa 12-14, 11001 Belgrade, Serbia.
| | - Milan M Milutinović
- University of Kragujevac, Institute for Information Technologies Kragujevac, Department of Natural Sciences, Jovana Cvijića bb, 34000 Kragujevac, Serbia; Institute for Inorganic and Analytical Chemistry, Technical University of Braunschweig, Hagenring 30, 38106 Braunschweig, Germany (present address)
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Aleksandar Tot
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Suzana Veličković
- Department of Physical Chemistry, Vinca Institute of Nuclear Sciences, University of Belgrade, Mike Petrovića Alasa 12-14, 11001 Belgrade, Serbia
| | - Žanka Bojić-Trbojević
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy, University of Belgrade, Banatska 31b, 11000 Zemun-Belgrade, Serbia
| | - Ana Rilak-Simović
- University of Kragujevac, Institute for Information Technologies Kragujevac, Department of Natural Sciences, Jovana Cvijića bb, 34000 Kragujevac, Serbia
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6
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Antiproliferative, DNA binding, and cleavage properties of dinuclear Co(III) complexes containing the bioactive quinizarin ligand. J Biol Inorg Chem 2020; 25:339-350. [DOI: 10.1007/s00775-020-01765-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/12/2020] [Indexed: 01/23/2023]
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7
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Kozsup M, Farkas E, Bényei AC, Kasparkova J, Crlikova H, Brabec V, Buglyó P. Synthesis, characterization and biological evaluation of Co(III) complexes with quinolone drugs. J Inorg Biochem 2019; 193:94-105. [DOI: 10.1016/j.jinorgbio.2019.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 11/27/2022]
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8
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Vadukul DM, Al-Hilaly YK, Serpell LC. Methods for Structural Analysis of Amyloid Fibrils in Misfolding Diseases. Methods Mol Biol 2019; 1873:109-122. [PMID: 30341606 DOI: 10.1007/978-1-4939-8820-4_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many proteins and peptides are able to self-assemble in solution in vitro and in vivo to form amyloid-like fibrils. These fibrils share common structural characteristics. In order for a fibril to be characterized as amyloid, it is expected to fit certain criteria including the composition of cross-β. Here we describe how the formation of amyloid fibrils can be characterized in vitro using a variety of methods including circular dichroism and intrinsic tyrosine/tryptophan fluoresence to follow conformational changes; Thioflavin and/or ThS assembly to monitor nucleation and growth; transmission electron microscopy to visualize fibrillar morphology and X-ray fiber diffraction to examine cross-β structure.
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Affiliation(s)
| | - Youssra K Al-Hilaly
- School of Life Sciences, University of Sussex, East Sussex, UK
- Department of Chemistry, College of Sciences, Al-Mustansiriyah University, Baghdad, Iraq
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9
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Dorrington G, Chmel NP, Norton SR, Wemyss AM, Lloyd K, Praveen Amarasinghe D, Rodger A. Light scattering corrections to linear dichroism spectroscopy for liposomes in shear flow using calcein fluorescence and modified Rayleigh-Gans-Debye-Mie scattering. Biophys Rev 2018; 10:1385-1399. [PMID: 30255222 PMCID: PMC6233352 DOI: 10.1007/s12551-018-0458-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/13/2018] [Indexed: 12/02/2022] Open
Abstract
The interpretation of data from absorbance spectroscopy experiments of liposomes in flow systems is often complicated by the fact that there is currently no easy way to account for scattering artefacts. This has proved particularly problematic for linear dichroism (LD) spectroscopy, which may be used to determine binding modes of small molecules, peptides and proteins to liposomes if we can extract the absorbance signal from the combined absorbance/scattering experiment. Equations for a modified Rayleigh-Gans-Debye (RGD) approximation to the turbidity (scattering) LD spectrum are available in the literature though have not been implemented. This review summarises the literature and shows how it can be implemented. The implementation proceeds by first determining volume loss that occurs when a spherical liposome is subjected to flow. Calcein fluorescence can be used for this purpose since at high concentrations (> 60 mM) it has low intensity fluorescence with maxima at 525 and 563 nm whereas at low concentrations (<1 mM) the fluorescence intensity is enhanced and the band shifts to 536 nm. The scattering calculation process yields the average axis ratios of the distorted liposome ellipsoids and extent of orientation of the liposomes in flow. The scattering calculations require methods to estimate liposome integrity, volume loss, and orientation when subjected to shear stresses under flow.
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Affiliation(s)
- Glen Dorrington
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Nikola P Chmel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Stephen R Norton
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Alan M Wemyss
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Katherine Lloyd
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - D Praveen Amarasinghe
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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10
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Rodger A, Dorrington G, Ang DL. Linear dichroism as a probe of molecular structure and interactions. Analyst 2018; 141:6490-6498. [PMID: 27840872 DOI: 10.1039/c6an01771a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear dichroism (LD) spectroscopy involves measuring the wavelength (or energy) dependence of the difference in absorption of light parallel and perpendicular to an orientation direction. It requires samples to have a net orientation. The aim of this review is to summarise some UV-visible linear dichroism (LD) methods that can be usefully applied to increase our understanding of biomacromolecules and their complexes that have a high aspect ratio. LD shares the advantages of most spectroscopic techniques including the fact that data collection is fairly straightforward and many sample types can be investigated. Conversely, LD shares the disadvantage that the measured signal is an average over all species in the sample on which the light beam is incident. LD mitigates this disadvantage somewhat in that only species which are oriented give a net signal. How the data can be analysed to give structural information about small molecules in stretched films and membrane systems or bound to biomacromolecules and directly about biomacromolecules such as DNA and protein fibres forms part of this review. In the UV-visible region LD often suffers noticeably from light scattering since the samples tend to be large relative to the wavelength of the incident light, so consideration is also given to data analysis challenges including removal of scattering contributions to an observed signal. Brief mention is made of fluorescence detected LD.
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Affiliation(s)
- Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Glen Dorrington
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Dale L Ang
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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11
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Wemyss AM, Chmel NP, Lobo DP, Sutherland JA, Dafforn TR, Rodger A. Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems. Chirality 2018; 30:227-237. [PMID: 29314266 DOI: 10.1002/chir.22795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/22/2017] [Accepted: 10/27/2017] [Indexed: 11/06/2022]
Abstract
Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the sample in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode. The role of the stray light reaching the detector that results in a spectral shape in fixed direct current mode that resembles the shape of a linear dichroism spectrum, rather than the expected reduced linear dichroism, is also explored.
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Affiliation(s)
- Alan M Wemyss
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Nikola P Chmel
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Daniela P Lobo
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - John A Sutherland
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia, USA
| | | | - Alison Rodger
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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12
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Pérez SA, de Haro C, Vicente C, Donaire A, Zamora A, Zajac J, Kostrhunova H, Brabec V, Bautista D, Ruiz J. New Acridine Thiourea Gold(I) Anticancer Agents: Targeting the Nucleus and Inhibiting Vasculogenic Mimicry. ACS Chem Biol 2017; 12:1524-1537. [PMID: 28388047 DOI: 10.1021/acschembio.7b00090] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two new 1-acridin-9-yl-3-methylthiourea Au(I) DNA intercalators [Au(ACRTU)2]Cl (2) and [Au(ACRTU) (PPh3)]PF6 (3) have been prepared. Both complexes were highly active in the human ovarian carcinoma cisplatin-sensitive A2780 cell line, exhibiting IC50 values in the submicromolar range. Compounds 2 and 3 are also cytotoxic toward different phenotypes of breast cancer cell lines MDA-MB-231 (triple negative), SK-BR-3 (HER2+, ERα-, and ERβ-), and MCF-7 (ER+). Both complexes induce apoptosis through activation of caspase-3 in vitro. While inhibition of some proteins (thiol-containing enzymes) seems to be the main mechanism of action for cytotoxic gold complexes, 2 and 3 present a DNA-dependent mechanism of action. They locate in the cell nucleus according to confocal microscopy and transmission electronic microscopy. The binding to DNA resulted to be via intercalation as shown by spectroscopic methods and viscometry, exhibiting a dose-dependent response on topoisomerase I mediated DNA unwinding. In addition, 2 and 3 exhibit potent antiangiogenic effects and are also able to inhibit vasculogenic mimicry of highly invasive MDA-MB-231 cells.
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Affiliation(s)
- Sergio A. Pérez
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
| | - Concepción de Haro
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
| | - Consuelo Vicente
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
| | - Antonio Donaire
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
| | - Ana Zamora
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
| | - Juraj Zajac
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic
- Department
of Biophysics, Faculty of Science, Palacky University, Slechtitelu
27, 783 71 Olomouc, Czech Republic
| | - Hana Kostrhunova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic
| | | | - José Ruiz
- Departamento
de Química Inorgánica, Facultad de Química, Biomedical
Research Institute of Murcia (IMIB-Arrixaca-UMU), Universidad de Murcia, E-30071 Murcia, Spain
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13
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Matsuo K, Maki Y, Namatame H, Taniguchi M, Gekko K. Conformation of membrane-bound proteins revealed by vacuum-ultraviolet circular-dichroism and linear-dichroism spectroscopy. Proteins 2016; 84:349-59. [PMID: 26756612 DOI: 10.1002/prot.24981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/09/2015] [Accepted: 12/19/2015] [Indexed: 12/16/2022]
Abstract
Knowledge of the conformations of a water-soluble protein bound to a membrane is important for understanding the membrane-interaction mechanisms and the membrane-mediated functions of the protein. In this study we applied vacuum-ultraviolet circular-dichroism (VUVCD) and linear-dichroism (LD) spectroscopy to analyze the conformations of α-lactalbumin (LA), thioredoxin (Trx), and β-lactoglobulin (LG) bound to phosphatidylglycerol liposomes. The VUVCD analysis coupled with a neural-network analysis showed that these three proteins have characteristic helix-rich conformations involving several helical segments, of which two amphiphilic or hydrophobic segments take part in interactions with the liposome. The LD analysis predicted the average orientations of these helix segments on the liposome: two amphiphilic helices parallel to the liposome surface for LA, two hydrophobic helices perpendicular to the liposome surface for Trx, and a hydrophobic helix perpendicular to and an amphiphilic helix parallel to the liposome surface for LG. This sequence-level information about the secondary structures and orientations was used to formulate interaction models of the three proteins at the membrane surface. This study demonstrates the validity of a combination of VUVCD and LD spectroscopy in conformational analyses of membrane-binding proteins, which are difficult targets for X-ray crystallography and nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Yasuyuki Maki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, 376-8515, Japan
| | - Hirofumi Namatame
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Masaki Taniguchi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan.,Department of Physical Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kunihiko Gekko
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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14
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The association of defensin HNP-2 with negatively charged membranes: A combined fluorescence and linear dichroism study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:892-903. [PMID: 26801370 DOI: 10.1016/j.bbamem.2016.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 01/09/2023]
Abstract
The association of defensin HNP-2 with negatively charged membranes has been studied using a new approach that combines fluorescence and linear dichroism (LD) spectroscopies with simulated LD spectra in order to characterise the binding kinetics and bound configurations of the peptide. Binding to membranes composed of mixtures of diacylglycerophosphocholines (PC) with either diacylglycerophosphoglycerol (PG) or diacylglycerophosphoserine (PS) was conducted at lipid:peptide ratios that yielded binding, but not membrane fusion. HNP-2 association with membranes under these conditions was a 2 stage-process, with both stages exhibiting first order kinetics. The fast initial step, with a half-life of < 1 min, was followed by a slower step with a half-life of > 3 min. Conversion between the states was estimated to have an enthalpy of activation of approximately 10 kJ mol(-1) and an entropy of activation of -0.2 kJ K mol(-1). LD spectra corresponding to each of the membrane bound states were generated by non-linear regression using a standard kinetic model. These spectra are interpreted in comparison with spectra calculated using the program Dichrocalc and reveal that the peptide associates with membranes in a small number of stable configurations. All of these configurations have a significant proportion of β-sheet structure residing in the plane of the membrane. Two configurations support structures previously proposed for defensins in membranes.
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15
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Holloway CR, Dyson RJ, Smith DJ. Linear Taylor–Couette stability of a transversely isotropic fluid. Proc Math Phys Eng Sci 2015. [DOI: 10.1098/rspa.2015.0141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fibre-laden fluids are found in a variety of situations, while Couette devices are used for flow spectroscopy of long biological molecules, such as DNA and proteins in suspension. The presence of these fibres can significantly alter the rheology of the fluid, and hence must be incorporated in any modelling undertaken. A transversely isotropic fluid treats these suspensions as a continuum with an evolving preferred direction, through a modified stress tensor incorporating four viscosity-like parameters. We consider the axisymmetric linear stability of a transversely isotropic viscous fluid, contained between two rotating co-axial cylinders, and determine the critical wave and Taylor numbers for varying gap width and inner cylinder velocity (assuming the outer cylinder is fixed). Through the inclusion of transversely isotropic effects, the onset of instability is delayed, increasing the range of stable operating regimes. This effect is felt most strongly through incorporation of the anisotropic shear viscosity, although the anisotropic extensional viscosity also contributes. The changes to the rheology induced by the presence of the fibres therefore significantly alter the dynamics of the system, and hence should not be neglected.
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Affiliation(s)
- C. R. Holloway
- School of Mathematics, University of Birmingham, Birmingham B15 2TT, UK
| | - R. J. Dyson
- School of Mathematics, University of Birmingham, Birmingham B15 2TT, UK
| | - D. J. Smith
- School of Mathematics, University of Birmingham, Birmingham B15 2TT, UK
- School of Engineering and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
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16
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Inhibition of DNA topoisomerases I and II and growth inhibition of HL-60 cells by novel acridine-based compounds. Eur J Pharm Sci 2015; 76:192-202. [PMID: 25960253 DOI: 10.1016/j.ejps.2015.04.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/04/2015] [Accepted: 04/25/2015] [Indexed: 11/20/2022]
Abstract
HL-60 cancer cells were treated with a series of novel acridine derivatives (derivatives 1-4) in order to test the compounds' ability to inhibit both cancer cell growth and topoisomerase I and II activity. Binding studies of derivatives 1-4 with calf thymus DNA were also performed using a number of techniques (UV-Vis and fluorescence spectroscopy, thermal denaturation, linear dichroism and viscometry) to determine the nature of the interaction between the compounds and ctDNA. The binding constants for the complexes of the studied acridine derivatives with DNA were calculated from UV-Vis spectroscopic titrations (K=3.1×10(4)-2.0×10(3)M(-1)). Some of the compounds showed a strong inhibitory effect against Topo II at the relatively low concentration of 5μM. Topo I/II inhibition mode assays were also performed and verified that the novel compounds are topoisomerase suppressors rather than poisons. The biological activities of derivatives were studied using MTT assay and flow cytometric methods (detection of mitochondrial membrane potential, measurement of cell viability) after 24 and 48h incubation. The ability of derivatives to impair cell proliferation was tested by an analysis of cell cycle distribution.
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17
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Tacrine derivatives as dual topoisomerase I and II catalytic inhibitors. Bioorg Chem 2015; 59:168-76. [DOI: 10.1016/j.bioorg.2015.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
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18
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Role of liposome and peptide in the synergistic enhancement of transfection with a lipopolyplex vector. Sci Rep 2015; 5:9292. [PMID: 25786833 PMCID: PMC4365389 DOI: 10.1038/srep09292] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/26/2015] [Indexed: 01/22/2023] Open
Abstract
Lipopolyplexes are of widespread interest for gene therapy due to their multifunctionality and high transfection efficiencies. Here we compared the biological and biophysical properties of a lipopolyplex formulation with its lipoplex and polyplex equivalents to assess the role of the lipid and peptide components in the formation and function of the lipopolyplex formulation. We show that peptide efficiently packaged plasmid DNA forming spherical, highly cationic nanocomplexes that are taken up efficiently by cells. However, transgene expression was poor, most likely due to endosomal degradation since the polyplex lacks membrane trafficking properties. In addition the strong peptide-DNA interaction may prevent plasmid release from the complex and so limit plasmid DNA availability. Lipid/DNA lipoplexes, on the other hand, produced aggregated masses that showed poorer cellular uptake than the polyplex but contrastingly greater levels of transgene expression. This may be due to the greater ability of lipoplexes relative to polyplexes to promote endosomal escape. Lipopolyplex formulations formed spherical, cationic nanocomplexes with efficient cellular uptake and significantly enhanced transfection efficiency. The lipopolyplexes combined the optimal features of lipoplexes and polyplexes showing optimal cell uptake, endosomal escape and availability of plasmid for transcription, thus explaining the synergistic increase in transfection efficiency.
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19
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Zsila F. Apparent circular dichroism signature of stirring-oriented DNA and drug–DNA complexes. Int J Biol Macromol 2015; 72:1034-40. [DOI: 10.1016/j.ijbiomac.2014.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/22/2014] [Accepted: 10/12/2014] [Indexed: 11/30/2022]
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20
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Ungvarsky J, Plsikova J, Janovec L, Koval J, Mikes J, Mikesová L, Harvanova D, Fedorocko P, Kristian P, Kasparkova J, Brabec V, Vojtickova M, Sabolova D, Stramova Z, Rosocha J, Imrich J, Kozurkova M. Novel trisubstituted acridines as human telomeric quadruplex binding ligands. Bioorg Chem 2014; 57:13-29. [PMID: 25171773 DOI: 10.1016/j.bioorg.2014.07.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 11/24/2022]
Abstract
A novel series of trisubstituted acridines were synthesized with the aim of mimicking the effects of BRACO19. These compounds were synthesized by modifying the molecular structure of BRACO19 at positions 3 and 6 with heteroacyclic moieties. All of the derivatives presented in the study exhibited stabilizing effects on the human telomeric DNA quadruplex. UV-vis spectroscopy, circular dichroism, linear dichroism and viscosimetry were used in order to study the nature of the DNA binding in more detail. The results show that all of the novel derivatives were able to fold the single-stranded DNA sequences into antiparallel G-quadruplex structures, with derivative 15 exhibiting the highest stabilizing capability. Cell cycle analysis revealed that a primary trend of the "braco"-like derivatives was to arrest the cells in the S- and G2M-phases of the cell cycle within the first 72h, with derivative 13 and BRACO19 proving particularly effective in suppressing cell proliferation. All studies derivatives were less toxic to human fibroblast cell line in comparison with HT 29 cancer cell line.
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Affiliation(s)
- Jan Ungvarsky
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jana Plsikova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic; Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Ladislav Janovec
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jan Koval
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jaromir Mikes
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Lucia Mikesová
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Denisa Harvanova
- Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Peter Fedorocko
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Pavol Kristian
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jana Kasparkova
- Institute of Biophysics, Department of Molecular Biophysics and Pharmacology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Department of Molecular Biophysics and Pharmacology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Maria Vojtickova
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Danica Sabolova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Zuzana Stramova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jan Rosocha
- Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Jan Imrich
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Maria Kozurkova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic.
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21
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Jiang T, Xu C, Liu Y, Liu Z, Wall JS, Zuo X, Lian T, Salaita K, Ni C, Pochan D, Conticello VP. Structurally defined nanoscale sheets from self-assembly of collagen-mimetic peptides. J Am Chem Soc 2014; 136:4300-8. [PMID: 24571053 DOI: 10.1021/ja412867z] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report the design of two collagen-mimetic peptide sequences, NSI and NSII, that self-assemble into structurally defined nanoscale sheets. The underlying structure of these nanosheets can be understood in terms of the layered packing of collagen triple helices in two dimensions. These nanosheet assemblies represent a novel morphology for collagen-based materials, which, on the basis of their defined structure, may be envisioned as potentially biocompatible platforms for controlled presentation of chemical functionality at the nanoscale. The molecularly programmed self-assembly of peptides NSI and NSII into nanosheets suggests that sequence-specific macromolecules offer significant promise as design elements for two-dimensional (2D) assemblies. This investigation provides a design rubric for fabrication of structurally defined, peptide-based nanosheets using the principles of solution-based self-assembly facilitated through complementary electrostatic interactions.
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Affiliation(s)
- Tao Jiang
- Department of Chemistry, Emory University , Atlanta, Georgia 30322
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22
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Lichen secondary metabolites as DNA-interacting agents. Toxicol In Vitro 2014; 28:182-6. [DOI: 10.1016/j.tiv.2013.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022]
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23
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Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP. Rational Design of Helical Nanotubes from Self-Assembly of Coiled-Coil Lock Washers. J Am Chem Soc 2013; 135:15565-78. [DOI: 10.1021/ja4074529] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunfu Xu
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Rui Liu
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Ricardo C. Guerrero-Ferreira
- Division
of Pediatric Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Suite 500, Atlanta, Georgia 30322, United States
| | - Elizabeth R. Wright
- Division
of Pediatric Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Suite 500, Atlanta, Georgia 30322, United States
| | - Stanislaw Dunin-Horkawicz
- Laboratory
of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, Warsaw 02-109, Poland
| | - Kyle Morris
- School
of Life Sciences, University of Sussex, Lewes Road, Falmer, East Sussex BN1
9QG, United Kingdom
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Lewes Road, Falmer, East Sussex BN1
9QG, United Kingdom
| | - Xiaobing Zuo
- X-ray
Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Joseph S. Wall
- Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, United States
| | - Vincent P. Conticello
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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24
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Morris KL, Rodger A, Hicks MR, Debulpaep M, Schymkowitz J, Rousseau F, Serpell LC. Exploring the sequence-structure relationship for amyloid peptides. Biochem J 2013; 450:275-83. [PMID: 23252554 PMCID: PMC3573774 DOI: 10.1042/bj20121773] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 01/10/2023]
Abstract
Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with 'steric-zipper' features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.
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Affiliation(s)
- Kyle L Morris
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
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25
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Daviter T, Chmel N, Rodger A. Circular and linear dichroism spectroscopy for the study of protein-ligand interactions. Methods Mol Biol 2013; 1008:211-241. [PMID: 23729254 DOI: 10.1007/978-1-62703-398-5_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Circular dichroism (CD) is the difference in absorption of left and right circularly polarized light, usually by a solution containing the molecules of interest. A non-zero signal for solutions is only measured for chiral molecules such as proteins whose mirror image is not superposable on the original molecule. A CD spectrum provides information about the bonds and structures responsible for the chirality. When a small molecule (or ligand) binds to a protein, it acquires an induced CD (ICD) spectrum through chiral perturbation to its structure or electron rearrangements (transitions). The wavelengths of this ICD are determined by the ligand's own absorption spectrum, and the intensity of the ICD spectrum is determined by the strength and geometry of its interaction with the protein. Thus, ICD can be used to probe the binding of ligands to proteins. This chapter contains an outline of how to perform protein CD and ICD experiments, together with some of the issues relating to experimental design and implementation. Addition of a quarter wave plate to a CD spectropolarimeter converts it to a linear dichroism (LD) spectrometer. When protein samples are aligned either in flow (as for fibers or membrane proteins in liposomes) or on surfaces the orientations of ligands with respect to the protein backbone or other subunits can be determined.
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Affiliation(s)
- Tina Daviter
- ISMB Biophysics Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
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26
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Mlcouskova J, Malina J, Novohradsky V, Kasparkova J, Komeda S, Brabec V. Energetics, conformation, and recognition of DNA duplexes containing a major adduct of an anticancer azolato-bridged dinuclear PtII complex. Biochim Biophys Acta Gen Subj 2012; 1820:1502-11. [DOI: 10.1016/j.bbagen.2012.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 05/25/2012] [Accepted: 05/30/2012] [Indexed: 11/24/2022]
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27
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3,6-bis(3-alkylguanidino)acridines as DNA-intercalating antitumor agents. Eur J Med Chem 2012; 57:283-95. [PMID: 23072739 DOI: 10.1016/j.ejmech.2012.09.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 11/20/2022]
Abstract
A series of 3,6-bis(3-alkylguanidino) acridines was prepared and the interaction of these novel compounds with calf thymus DNA was investigated with UV-vis, fluorescence and circular dichroism spectroscopy, in addition to DNA melting techniques. The binding constants K were estimated to range from 1.25 to 5.26 × 10(5) M(-1), and the percentage of hypochromism was found to be 17-42% (from spectral titration). UV-vis, fluorescence and circular dichroism measurements indicated that the compounds act as effective DNA-intercalating agents. Electrophoretic separation proved that ligands 6a-e relaxed topoisomerase I at a concentration of 60 μM, although only those with longer alkyl chains were able to penetrate cell membranes and suppress cell proliferation effectively. The biological activity of novel compounds was assessed using different techniques (cell cycle distribution, phosphatidylserine externalization, caspase-3 activation, changes in mitochondrial membrane potential) and demonstrated mostly transient cytostatic action of the ethyl 6c and pentyl 6d derivatives. The hexyl derivative 6e proved to be the most cytotoxic. Different patterns of cell penetration were also observed for individual derivatives. Principles of molecular dynamics were applied to explore DNA-ligand interactions at the molecular level.
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28
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Cerasoli E, Ravi J, Gregor C, Hussain R, Siligardi G, Martyna G, Crain J, Ryadnov MG. Membrane mediated regulation in free peptides of HIV-1 gp41: minimal modulation of the hemifusion phase. Phys Chem Chem Phys 2012; 14:1277-85. [DOI: 10.1039/c1cp23155c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Calero M, Gasset M. Featuring amyloids with Fourier transform infrared and circular dichroism spectroscopies. Methods Mol Biol 2012; 849:53-68. [PMID: 22528083 DOI: 10.1007/978-1-61779-551-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Amyloids are fibrillar aggregates of proteins characterized by a basic scaffold consisting of cross β-sheet structure that can exert physiological or pathological effects. Both far-UV circular dichroism and Fourier transform infrared (FTIR) spectroscopies are techniques used for the fast analysis of protein secondary structure. Both techniques are complementary and preferentially used depending on the physical state of the analyte, the major secondary structure element and the relative abundance of given amino acids. Although there are special setups for working with films, circular dichroism is best suited for ideal diluted solutions of polypeptides exhibiting α-helix as major structural element and low content of aromatic residues. During the last decade, a related technique, linear dichroism, has been applied to study the orientation of protein subunits within amyloid oligomers or fibrils in solution. Alternatively, FTIR works best with concentrated solutions, solids and films, and resolves with accuracy the β-sheet composition, but it is affected by contributions of amide groups. The advent of new infrared techniques based on correlation analysis of time-dependent variations induced by external perturbations that generates two-dimensional IR maps has enabled to greatly increase spectral resolution and to extend its applicability to protein secondary structure characterization in a variety of physical environments. Within the amyloid field, conjunction of both spectroscopies has provided the first filter step for amyloid detection and has contributed to decipher the structural aspects of the amyloid formation mechanism.
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Affiliation(s)
- Miguel Calero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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30
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Pacheco-Gómez R, Kraemer J, Stokoe S, England HJ, Penn CW, Stanley E, Rodger A, Ward J, Hicks MR, Dafforn TR. Detection of Pathogenic Bacteria Using a Homogeneous Immunoassay Based on Shear Alignment of Virus Particles and Linear Dichroism. Anal Chem 2011; 84:91-7. [PMID: 22017566 DOI: 10.1021/ac201544h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Raúl Pacheco-Gómez
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Julia Kraemer
- TU Dresden, Institut für Lebensmittel- und Bioverfahrenstechnik (Institute of Food Technology and Bioprocess Engineering) 01062 Dresden
| | - Susan Stokoe
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Hannah J. England
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Charles W. Penn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
| | - Emma Stanley
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, Warwickshire, CV4 7AL, U.K
| | - John Ward
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, U.K
| | - Matthew R. Hicks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
- Department of Chemistry, University of Warwick, Coventry, Warwickshire, CV4 7AL, U.K
| | - Timothy R. Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, U.K
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31
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Macchi F, Hoffmann SV, Carlsen M, Vad B, Imparato A, Rischel C, Otzen DE. Mechanical stress affects glucagon fibrillation kinetics and fibril structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12539-12549. [PMID: 21877745 DOI: 10.1021/la202125c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mechanical stress can strongly influence the capability of a protein to aggregate and the kinetics of aggregation, but there is little insight into the underlying mechanism. Here we study the effect of different mechanical stress conditions on the fibrillation of the peptide hormone glucagon, which forms different fibrils depending on temperature, pH, ionic strength, and concentration. A combination of spectroscopic and microscopic data shows that fibrillar polymorphism can also be induced by mechanical stress. We observed two classes of fibrils: a low-stress and a high-stress class, which differ in their kinetic profiles, secondary structure as well as morphology and that are able to self-propagate in a template-dependent fashion. The bending rigidity of the low-stress fibrils is sensitive to the degree of mechanical perturbation. We propose a fibrillation model, where interfaces play a fundamental role in the switch between the two fibrillar classes. Our work also raises the cautionary note that mechanical perturbation is a potential source of variability in the study of fibrillation mechanisms and fibril structures.
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Affiliation(s)
- Francesca Macchi
- iNANO, Center for Insoluble Protein Structures (inSPIN), Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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32
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Buell AK, Esbjörner EK, Riss PJ, White DA, Aigbirhio FI, Toth G, Welland ME, Dobson CM, Knowles TPJ. Probing small molecule binding to amyloid fibrils. Phys Chem Chem Phys 2011; 13:20044-52. [PMID: 22006124 DOI: 10.1039/c1cp22283j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.
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Affiliation(s)
- Alexander K Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Kostrhunova H, Malina J, Pickard AJ, Stepankova J, Vojtiskova M, Kasparkova J, Muchova T, Rohlfing ML, Bierbach U, Brabec V. Replacement of a thiourea with an amidine group in a monofunctional platinum-acridine antitumor agent. Effect on DNA interactions, DNA adduct recognition and repair. Mol Pharm 2011; 8:1941-54. [PMID: 21806015 DOI: 10.1021/mp200309x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A combination of biophysical, biochemical, and computational techniques was used to delineate mechanistic differences between the platinum-acridine hybrid agent [PtCl(en)(L)](NO(3))(2) (complex 1, en = ethane-1,2-diamine, L = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) and a considerably more potent second-generation analogue containing L' = N-[2-(acridin-9-ylamino)ethyl]-N-methylpropionamidine (complex 2). Calculations at the density functional theory level provide a rationale for the binding preference of both complexes for guanine-N7 and the relatively high level of adenine adducts observed for compound 1. A significant rate enhancement is observed for binding of the amidine-based complex 2 with DNA compared with the thiourea-based prototype 1. Studies conducted with chemical probes and on the bending and unwinding of model duplex DNA suggest that adducts of complex 2 perturb B-form DNA more severely than complex 1, however, without denaturing the double strand and significantly less than cisplatin. Circular and linear dichroism spectroscopies and viscosity measurements suggest that subtle differences exist between the intercalation modes and adduct geometries of the two complexes. The adducts formed by complex 2 most efficiently inhibit transcription of the damaged DNA by RNA polymerase II. Not only do complexes 1 and 2 cause less distortion to DNA than cisplatin, they also do not compromise the thermodynamic stability of the modified duplex. This leads to a decreased or negligible affinity of HMG domain proteins for the adducts formed by either Pt-acridine complex. In a DNA repair synthesis assay the lesions formed by complex 2 were repaired less efficiently than those formed by complex 1. These significant differences in DNA adduct formation, structure, and recognition between the two acridine complexes and cisplatin help to elucidate why compound 2 is highly active in cisplatin-resistant, repair proficient cancer cell lines.
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Affiliation(s)
- Hana Kostrhunova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi Kralovopolska 135, CZ-61265 Brno, Czech Republic
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DNA interactions of 2-pyrrolinodoxorubicin, a distinctively more potent daunosamine-modified analogue of doxorubicin. Biochem Pharmacol 2011; 82:227-35. [DOI: 10.1016/j.bcp.2011.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/03/2011] [Accepted: 04/26/2011] [Indexed: 11/18/2022]
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36
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Marshall KE, Hicks MR, Williams TL, Hoffmann SV, Rodger A, Dafforn TR, Serpell LC. Characterizing the assembly of the Sup35 yeast prion fragment, GNNQQNY: structural changes accompany a fiber-to-crystal switch. Biophys J 2010; 98:330-8. [PMID: 20338855 DOI: 10.1016/j.bpj.2009.10.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/13/2009] [Accepted: 10/15/2009] [Indexed: 01/18/2023] Open
Abstract
Amyloid-like fibrils can be formed by many different proteins and peptides. The structural characteristics of these fibers are very similar to those of amyloid fibrils that are deposited in a number of protein misfolding diseases, including Alzheimer's disease and the transmissible spongiform encephalopathies. The elucidation of two crystal structures from an amyloid-like fibril-forming fragment of the yeast prion, Sup35, with sequence GNNQQNY, has contributed to knowledge regarding side-chain packing of amyloid-forming peptides. Both structures share a cross-beta steric zipper arrangement but vary in the packing of the peptide, particularly in terms of the tyrosine residue. We investigated the fibrillar and crystalline structure and assembly of the GNNQQNY peptide using x-ray fiber diffraction, electron microscopy, intrinsic and quenched tyrosine fluorescence, and linear dichroism. Electron micrographs reveal that at concentrations between 0.5 and 10 mg/mL, fibers form initially, followed by crystals. Fluorescence studies suggest that the environment of the tyrosine residue changes as crystals form. This is corroborated by linear dichroism experiments that indicate a change in the orientation of the tyrosine residue over time, which suggests that a structural rearrangement occurs as the crystals form. Experimental x-ray diffraction patterns from fibers and crystals also suggest that these species are structurally distinct. A comparison of experimental and calculated diffraction patterns contributes to an understanding of the different arrangements accessed by the peptide.
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Affiliation(s)
- Karen E Marshall
- Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, United Kingdom
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Hamley IW, Castelletto V, Moulton CM, Rodríguez-Pérez J, Squires AM, Eralp T, Held G, Hicks MR, Rodger A. Alignment of a Model Amyloid Peptide Fragment in Bulk and at a Solid Surface. J Phys Chem B 2010; 114:8244-54. [DOI: 10.1021/jp101374e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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38
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Hicks MR, Kowałski J, Rodger A. LD spectroscopy of natural and synthetic biomaterials. Chem Soc Rev 2010; 39:3380-93. [DOI: 10.1039/b912917k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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39
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Abstract
When a drug binds to DNA, its electronic structure is perturbed, and it perturbs the DNA's electronic structure. The resulting change to the electronic spectroscopy can be used to probe the drug-DNA interaction. This chapter outlines how circular and linear dichroism spectroscopy can be used to provide information about drug-DNA systems. Circular dichroism spectroscopy involves measuring the difference in absorption of left and right circularly polarized light. It is uniquely sensitive to the helicity of the molecules being studied. Linear dichroism, as the name implies, involves measuring the difference in absorption of light linearly polarized parallel and perpendicular to an orientation axis. Linear dichroism provides information about the relative orientations of subunits of an interacting system. The material presented in this chapter is by no means comprehensive; the aim is to enable the user to collect reasonable quality data and to interpret it.
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Affiliation(s)
- Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, UK.
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Bulheller BM, Rodger A, Hicks MR, Dafforn TR, Serpell LC, Marshall KE, Bromley EHC, King PJS, Channon KJ, Woolfson DN, Hirst JD. Flow Linear Dichroism of Some Prototypical Proteins. J Am Chem Soc 2009; 131:13305-14. [DOI: 10.1021/ja902662e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin M. Bulheller
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Alison Rodger
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Matthew R. Hicks
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Timothy R. Dafforn
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Louise C. Serpell
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Karen E. Marshall
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Elizabeth H. C. Bromley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Patrick J. S. King
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Kevin J. Channon
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K., Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K., Department of Biochemistry, School of Life Sciences, University of Sussex, Falmer BN1 9QG, U.K., School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K., and Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
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Childers WS, Mehta AK, Lu K, Lynn DG. Templating Molecular Arrays in Amyloid’s Cross-β Grooves. J Am Chem Soc 2009; 131:10165-72. [DOI: 10.1021/ja902332s] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- W. Seth Childers
- Center for Fundamental and Applied Molecular Evolution (FAME), and Department of Chemistry and Biology, Emory University, Atlanta, Georgia 30322
| | - Anil K. Mehta
- Center for Fundamental and Applied Molecular Evolution (FAME), and Department of Chemistry and Biology, Emory University, Atlanta, Georgia 30322
| | - Kun Lu
- Center for Fundamental and Applied Molecular Evolution (FAME), and Department of Chemistry and Biology, Emory University, Atlanta, Georgia 30322
| | - David G. Lynn
- Center for Fundamental and Applied Molecular Evolution (FAME), and Department of Chemistry and Biology, Emory University, Atlanta, Georgia 30322
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42
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Ennaceur SM, Hicks MR, Pridmore CJ, Dafforn TR, Rodger A, Sanderson JM. Peptide adsorption to lipid bilayers: slow processes revealed by linear dichroism spectroscopy. Biophys J 2009; 96:1399-407. [PMID: 19217857 DOI: 10.1016/j.bpj.2008.10.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 10/28/2008] [Indexed: 12/16/2022] Open
Abstract
The adsorption and insertion kinetics for the association of two 34-residue cyclic peptides with phosphocholine membranes have been studied using circular and linear dichroism approaches. The two peptides studied are identical with the exception of two residues, which are both tyrosine in one of the peptides and tryptophan in the other. Both peptides adopt random coil conformations in solution in the absence of membranes and do not aggregate at concentrations below 20 microM. After addition to liposome dispersions, circular dichroism spectroscopy indicated that both peptides undergo an extremely rapid transformation to a beta-conformation that remains unchanged throughout the remainder of the experiment. Linear dichroism (LD) spectroscopy was used to study the kinetics of membrane adsorption and insertion. The data were analyzed by nonlinear least squares approaches, leading to identification of a number of bound states and their corresponding LD spectra. Two pseudo-first order processes could be identified that were common to both peptides. The first occurred with a time constant of the order of 1 min and led to a bound state characterized by weak LD signals, with significant bands corresponding to the transitions of aromatic side chains. The second process occurred with an unusually long time constant of between 75 and 100 min, forming a state with considerably stronger positive LD absorbance in the far-ultraviolet region of the spectrum. For the tyrosine-substituted peptide, a third slow process with a long time constant (76 min) could also be delineated and was attributed to rearrangements of the peptide within the membrane.
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Affiliation(s)
- Sue M Ennaceur
- Department of Chemistry, University Science Laboratories, Durham, DH1 3LE, United Kingdom
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43
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Rittman M, Gilroy E, Koohy H, Rodger A, Richards A. Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review. Sci Prog 2009; 92:163-204. [PMID: 19697713 PMCID: PMC10361128 DOI: 10.3184/003685009x462205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.
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Affiliation(s)
- Martyn Rittman
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Emma Gilroy
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Hashem Koohy
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Adair Richards
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
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44
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Corral E, Hotze ACG, den Dulk H, Leczkowska A, Rodger A, Hannon MJ, Reedijk J. Ruthenium polypyridyl complexes and their modes of interaction with DNA: is there a correlation between these interactions and the antitumor activity of the compounds? J Biol Inorg Chem 2008; 14:439-48. [PMID: 19085018 PMCID: PMC3036821 DOI: 10.1007/s00775-008-0460-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 12/02/2008] [Indexed: 11/04/2022]
Abstract
Various interaction modes between a group of six ruthenium polypyridyl complexes and DNA have been studied using a number of spectroscopic techniques. Five mononuclear species were selected with formula [Ru(tpy)L1L2](2−n)+, and one closely related dinuclear cation of formula [{Ru(apy)(tpy)}2{μ-H2N(CH2)6NH2}]4+. The ligand tpy is 2,2′:6′,2″-terpyridine and the ligand L1 is a bidentate ligand, namely, apy (2,2′-azobispyridine), 2-phenylazopyridine, or 2-phenylpyridinylmethylene amine. The ligand L2 is a labile monodentate ligand, being Cl−, H2O, or CH3CN. All six species containing a labile L2 were found to be able to coordinate to the DNA model base 9-ethylguanine by 1H NMR and mass spectrometry. The dinuclear cationic species, which has no positions available for coordination to a DNA base, was studied for comparison purposes. The interactions between a selection of four representative complexes and calf-thymus DNA were studied by circular and linear dichroism. To explore a possible relation between DNA-binding ability and toxicity, all compounds were screened for anticancer activity in a variety of cancer cell lines, showing in some cases an activity which is comparable to that of cisplatin. Comparison of the details of the compound structures, their DNA binding, and their toxicity allows the exploration of structure–activity relationships that might be used to guide optimization of the activity of agents of this class of compounds.
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Affiliation(s)
- Eva Corral
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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45
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Lee CC, Grenier C, Meijer EW, Schenning APHJ. Preparation and characterization of helical self-assembled nanofibers. Chem Soc Rev 2008; 38:671-83. [PMID: 19322461 DOI: 10.1039/b800407m] [Citation(s) in RCA: 283] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This tutorial review serves as an introduction to helical self-assembled systems, illustrated by a specific class of helical aggregates: helical nanofibers. The common ways by which these systems are designed, prepared, and characterized will be presented.
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Affiliation(s)
- Cameron C Lee
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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46
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Breaking the 200 nm limit for routine flow linear dichroism measurements using UV synchrotron radiation. Biophys J 2008; 95:5974-7. [PMID: 18805928 DOI: 10.1529/biophysj.108.139964] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first synchrotron radiation flow linear dichroism spectra are reported. High-quality spectral data can be collected from 450 nm down to 180 nm in contrast to the practical cutoff of approximately 200 nm on benchtop instruments. State-of-the-art microvolume capillary Couette flow linear dichroism was successfully ported to a synchrotron radiation source. The sample volume required is < 50 microL. A characterization of the synchrotron radiation linear dichroism with known DNA and DNA-ligand systems is presented and the viability of the setup confirmed. Typically, wavelengths down to 180 nm are now routinely accessible with a high signal/noise ratio with little limitation from the sample concentration. The 180 nm cutoff is due to the quartz of the Couette cell rather than the beamline itself. We show the application of the simultaneous determination of the sample absorption spectrum to calculate the reduced linear dichroism signal. Spectra for calf thymus DNA, DNA/ethidium bromide, and DNA/4',6-diamidino-2-phenylindole systems illustrate the quality of data that can be obtained.
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47
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Bugarcic T, Nováková O, Zerzánková L, Vrána O, Kašpárková J, Habtemariam A, Parsons S, Sadler PJ, Brabec V. Cytotoxicity, Cellular Uptake, and DNA Interactions of New Monodentate Ruthenium(II) Complexes Containing Terphenyl Arenes. J Med Chem 2008; 51:5310-9. [DOI: 10.1021/jm8003043] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tijana Bugarcic
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Olga Nováková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Lenka Zerzánková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Oldřich Vrána
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Jana Kašpárková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Abraha Habtemariam
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Simon Parsons
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Peter J. Sadler
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Viktor Brabec
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
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Casey JP, Bachilo SM, Moran CH, Weisman RB. Chirality-resolved length analysis of single-walled carbon nanotube samples through shear-aligned photoluminescence anisotropy. ACS NANO 2008; 2:1738-1746. [PMID: 19206379 DOI: 10.1021/nn800351n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An efficient new method is demonstrated for measuring length distributions of semiconducting single-walled carbon nanotubes (SWCNTs) through analysis of their highly polarized photoluminescence when aligned by shear flows. Instrumentation and procedures are developed to characterize nanotube lengths in bulk suspensions with rapid data acquisition and interpretation. Applying the method with spectrally resolved SWCNT emission provides the first measurements of (n,m)-specific length distributions. A positive correlation is found between average length and nanotube diameter, although this correlation is weaker following extensive sample centrifugation. Intense sonication shortened all nanotube species and had the strongest effect on those with small diameters. The new method should provide a useful alternative to atomic force microscopy for characterizing SWCNT lengths.
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Affiliation(s)
- John P Casey
- Department of Chemistry, Richard E. Smalley Institute for Nanoscale Science and Technology, Rice University, Houston, Texas 77005, USA
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