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Xu X, Closson JD, Marcelino LP, Favaro DC, Silvestrini ML, Solazzo R, Chong LT, Gardner KH. Identification of small-molecule ligand-binding sites on and in the ARNT PAS-B domain. J Biol Chem 2024; 300:107606. [PMID: 39059491 PMCID: PMC11381877 DOI: 10.1016/j.jbc.2024.107606] [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: 06/11/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Transcription factors are challenging to target with small-molecule inhibitors due to their structural plasticity and lack of catalytic sites. Notable exceptions include naturally ligand-regulated transcription factors, including our prior work with the hypoxia-inducible factor (HIF)-2 transcription factor, showing that small-molecule binding within an internal pocket of the HIF-2α Per-Aryl hydrocarbon Receptor Nuclear Translocator (ARNT)-Sim (PAS)-B domain can disrupt its interactions with its dimerization partner, ARNT. Here, we explore the feasibility of targeting small molecules to the analogous ARNT PAS-B domain itself, potentially opening a promising route to modulate several ARNT-mediated signaling pathways. Using solution NMR fragment screening, we previously identified several compounds that bind ARNT PAS-B and, in certain cases, antagonize ARNT association with the transforming acidic coiled-coil containing protein 3 transcriptional coactivator. However, these ligands have only modest binding affinities, complicating characterization of their binding sites. We address this challenge by combining NMR, molecular dynamics simulations, and ensemble docking to identify ligand-binding "hotspots" on and within the ARNT PAS-B domain. Our data indicate that the two ARNT/transforming acidic coiled-coil containing protein 3 inhibitors, KG-548 and KG-655, bind to a β-sheet surface implicated in both HIF-2 dimerization and coactivator recruitment. Furthermore, while KG-548 binds exclusively to the β-sheet surface, KG-655 can additionally bind within a water-accessible internal cavity in ARNT PAS-B. Finally, KG-279, while not a coactivator inhibitor, exemplifies ligands that preferentially bind only to the internal cavity. All three ligands promoted ARNT PAS-B homodimerization, albeit to varying degrees. Taken together, our findings provide a comprehensive overview of ARNT PAS-B ligand-binding sites and may guide the development of more potent coactivator inhibitors for cellular and functional studies.
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Affiliation(s)
- Xingjian Xu
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD Program in Biochemistry, The Graduate Center, CUNY, New York, New York, USA
| | - Joseph D Closson
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; PhD Program in Biochemistry, The Graduate Center, CUNY, New York, New York, USA
| | | | - Denize C Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Marion L Silvestrini
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Riccardo Solazzo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Bologna, Italy
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, New York, USA; PhD. Programs in Biochemistry, Chemistry and Biology, The Graduate Center, CUNY, New York, New York, USA.
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2
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Mori I, Terasaka S, Yamaguchi S, Otosu T. Diffusion of Multiple Species Resolved by Fluorescence Lifetime Recovery after Photobleaching (FLRAP). Anal Chem 2024; 96:4854-4859. [PMID: 38497530 DOI: 10.1021/acs.analchem.3c05181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Fluorescence recovery after photobleaching (FRAP) is now an indispensable tool to analyze the diffusion of molecules in vivo and in vitro. However, a conventional fluorescence intensity-based approach has difficulty in analyzing the diffusion of multiple species simultaneously. Here, we report fluorescence lifetime recovery after photobleaching (FLRAP) that incorporates fluorescence lifetime information into FRAP. By using FLRAP, the fluorescence intensity-recovery curves of each species can be successfully extracted from the ensemble photon data by utilizing their species-specific fluorescence decay curves, which are verified by applying FLRAP to two heterogeneous systems. Thus, FLRAP can be a powerful tool to quantitatively elucidate the molecular diffusion of multiple species in complex systems such as in living cells.
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Affiliation(s)
- Ikumi Mori
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shun Terasaka
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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3
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Gilboa T, Swank Z, Thakur R, Gould RA, Ooi KH, Norman M, Flynn EA, Deveney BT, Chen A, Borberg E, Kuzkina A, Ndayisaba A, Khurana V, Weitz DA, Walt DR. Toward the quantification of α-synuclein aggregates with digital seed amplification assays. Proc Natl Acad Sci U S A 2024; 121:e2312031121. [PMID: 38194461 PMCID: PMC10801878 DOI: 10.1073/pnas.2312031121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024] Open
Abstract
The quantification and characterization of aggregated α-synuclein in clinical samples offer immense potential toward diagnosing, treating, and better understanding neurodegenerative synucleinopathies. Here, we developed digital seed amplification assays to detect single α-synuclein aggregates by partitioning the reaction into microcompartments. Using pre-formed α-synuclein fibrils as reaction seeds, we measured aggregate concentrations as low as 4 pg/mL. To improve our sensitivity, we captured aggregates on antibody-coated magnetic beads before running the amplification reaction. By first characterizing the pre-formed fibrils with transmission electron microscopy and size exclusion chromatography, we determined the specific aggregates targeted by each assay platform. Using brain tissue and cerebrospinal fluid samples collected from patients with Parkinson's Disease and multiple system atrophy, we demonstrated that the assay can detect endogenous pathological α-synuclein aggregates. Furthermore, as another application for these assays, we studied the inhibition of α-synuclein aggregation in the presence of small-molecule inhibitors and used a custom image analysis pipeline to quantify changes in aggregate growth and filament morphology.
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Affiliation(s)
- Tal Gilboa
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Zoe Swank
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Rohan Thakur
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
- Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Russell A. Gould
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Kean Hean Ooi
- Department of Medical Sciences, Harvard Medical School, Boston, MA02115
| | - Maia Norman
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
- Physician Scientist Training Program, Massachusetts General Hospital/McLean Residency in Adult Psychiatry, Boston, MA02114
| | - Elizabeth A. Flynn
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Brendan T. Deveney
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
| | - Anqi Chen
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
| | - Ella Borberg
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Anastasia Kuzkina
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
| | - Alain Ndayisaba
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
| | - Vikram Khurana
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
- Harvard Stem Cell Institute, Cambridge, MA02138
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - David A. Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
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4
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Palicha KA, Loganathan P, Sudha V, Harinipriya S. Monte Carlo simulation and experimental validation of plant microtubules cathode in biodegradable battery. Sci Rep 2023; 13:10393. [PMID: 37369685 DOI: 10.1038/s41598-023-36902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
For the first time, electrochemical methods are utilized to study the response of tubulin monomers (extracted from plant source such as Green Peas: Arachis Hypogea) towards charge perturbations in the form of conductivity, conformational changes via self-assembly and adsorption on Au surface. The obtained dimerization and surface adsorption energetics of the tubulins from Cyclic Voltammetry agree well with the literature value of 6.9 and 14.9 kCal/mol for lateral and longitudinal bond formation energy respectively. In addition to the effects of charge perturbations on change in structure, ionic and electronic conductivity of tubulin with increasing load are investigated and found to be 1.25 Sm-1 and 2.89 mSm-1 respectively. The electronic conductivity is 1.93 times higher than the literature value of 1.5 mSm-1, demonstrating the fact that the microtubules (dimer of tubulins, MTs) from plant source can be used as a semiconductor electrode material in energy conversion and storage applications. Thus, motivated by the Monte Carlo simulation and electrochemical results the MTs extracted from plant source are used as cathode material for energy storage device such as Bio-battery and the Galvanostatic Charge/Discharge studies are carried out in coin cell configuration. The configuration of the bio-battery cell is as follows: Al/CB//PP-1M KCl//MTs/SS; where SS and Al are used as current collectors for cathode and anode respectively, Polypropylene (PP) membrane soaked in 1M KCl as electrolyte and Carbon Black (CB) is the anode material. Another configuration of the cell would be replacement of CB by biopolymer such as ethyl cellulose anode (Al/EC/PP-1M KCl/MTs/SS).
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Affiliation(s)
- Kaushik A Palicha
- Research and Development Center, Ram Charan Co Pvt Ltd - Entity1, Chennai, Tamilnadu, 600 002, India
| | - Pavithra Loganathan
- Department of Physics and Nanotechnology, SRMIST, Kattankulathur, Chennai, Tamilnadu, 603203, India
| | - V Sudha
- Department of Chemistry, SRMIST, Kattankulathur, Chennai, Tamilnadu, 603203, India.
| | - S Harinipriya
- Research and Development Center, Ram Charan Co Pvt Ltd - Entity1, Chennai, Tamilnadu, 600 002, India.
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Long X, Tokunou Y, Okamoto A. Mechano-control of Extracellular Electron Transport Rate via Modification of Inter-heme Coupling in Bacterial Surface Cytochrome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7421-7430. [PMID: 37079493 DOI: 10.1021/acs.est.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial outer-membrane multi-heme cytochromes (OMCs) mediate extracellular electron transport (EET). While heme alignment dictates the rate of EET, control of inter-heme coupling in a single OMC remains challenging, especially in intact cells. Given that OMCs diffuse and collide without aggregation on the cell surface, the overexpression of OMCs could increase such mechanical stress to impact the OMCs' protein structure. Here, the heme coupling is modified via mechanical interactions among OMCs by controlling their concentrations. Employment of whole-cell circular dichroism (CD) spectra of genetically engineered Escherichia coli reveals that the OMC concentration significantly impacts the molar CD and redox property of OMCs, resulting in a 4-fold change of microbial current production. The overexpression of OMCs increased the conductive current across the biofilm on an interdigitated electrode, indicating that a higher concentration of OMCs causes more lateral inter-protein electron hopping via collision on the cell surface. The present study would open a novel strategy to increase microbial current production by mechanically enhancing the inter-heme coupling.
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Affiliation(s)
- Xizi Long
- School of the Key Laboratory of Typical Environmental Pollution and Health Hazards of Hunan Province, School of Basic Medicine, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Yoshihide Tokunou
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kitaku, Sapporo, Hokkaido 060-8628, Japan
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6
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Ma G, Zhang P, Zhou X, Wan Z, Wang S. Label-Free Single-Molecule Pulldown for the Detection of Released Cellular Protein Complexes. ACS CENTRAL SCIENCE 2022; 8:1272-1281. [PMID: 36188347 PMCID: PMC9523780 DOI: 10.1021/acscentsci.2c00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 06/16/2023]
Abstract
Precise and sensitive detection of intracellular proteins and complexes is key to the understanding of signaling pathways and cell functions. Here, we present a label-free single-molecule pulldown (LFSMP) technique for the imaging of released cellular protein and protein complexes with single-molecule sensitivity and low sample consumption down to a few cells per mm2. LFSMP is based on plasmonic scattering imaging and thus can directly image the surface-captured molecules without labels and quantify the binding kinetics. In this paper, we demonstrate the detection principle for LFSMP, study the phosphorylation of protein complexes involved in a signaling pathway, and investigate how kinetic analysis can be used to improve the pulldown specificity. We wish our technique can contribute to uncovering the molecular mechanisms in cells with single-molecule resolution.
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Affiliation(s)
- Guangzhong Ma
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Zhang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xinyu Zhou
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Zijian Wan
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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7
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Fan HF, Chen WL, Chen YZ, Huang JW, Shen YX. Change in the Oligomeric State of α-Synuclein Variants in Living Cells. ACS Chem Neurosci 2022; 13:1143-1164. [PMID: 35394271 DOI: 10.1021/acschemneuro.1c00646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The accumulation of β-sheet-rich α-synuclein (α-Syn) protein in human brain cells is a pathological hallmark of Parkinson's disease (PD). Moreover, it has been reported that familial PD mutations (A30P, E46K, H50Q, G51D, and A53T) accumulate at an accelerated rate both in vivo and in vitro. In addition, accumulations of various C-terminal α-Syn truncations, such as C-terminal-truncated N103 α-synuclein (N103), were found in an aggregated form in the brain tissue of PD patients. Fluorescent protein-tagged wild-type α-Syn, A30P, E46K, H50Q, G51D, A53T, and N103 were transfected into HEK293T and SHSY5Y cells, and their diffusion behaviors were investigated with a custom-built fluorescence microscope system. Based on our experimental results, the oligomerization of α-Syn is a time-dependent process in both HEK293T and SHSY5Y cells, and the oligomer state approaches a plateau after 48 h of transfection. The change in the oligomeric state of E46K, H50Q, and G51D exhibited a similar trend to the wild type at a lower concentration but became intense at a higher concentration. A53T and N103 possess smaller diffusion coefficients than wild-type α-synuclein and other family PD mutations, indicating that these two mutants could form higher oligomeric states or stronger interactions in HEK293T and SHSY5Y cells. In contrast, the smallest oligomer and the lowest intracellular interaction among all investigated α-Syn variants were found for A30P. These phenomena indicated the presence of different pathogeneses among familial PD mutants and C-terminal α-Syn truncations.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
- Aerosol Science Research Center, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
| | - Wen-Ling Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei 112, Taiwan
| | - Yan-Zhow Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Section 2, Linong Street, Taipei 112, Taiwan
| | - Jian-Wei Huang
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
| | - Yu-Xin Shen
- Department of Chemistry, National Sun Yat-sen University, No. 70 Lien-hai Road, Kaohsiung 80424, Kaohsiung 804, Taiwan
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Vala M, Bujak Ł, García Marín A, Holanová K, Henrichs V, Braun M, Lánský Z, Piliarik M. Nanoscopic Structural Fluctuations of Disassembling Microtubules Revealed by Label-Free Super-Resolution Microscopy. SMALL METHODS 2021; 5:e2000985. [PMID: 34927839 DOI: 10.1002/smtd.202000985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/22/2020] [Indexed: 06/14/2023]
Abstract
Microtubules are cytoskeletal polymers of tubulin dimers assembled into protofilaments that constitute nanotubes undergoing periods of assembly and disassembly. Static electron micrographs suggest a structural transition of straight protofilaments into curved ones occurring at the tips of disassembling microtubules. However, these structural transitions have never been observed and the process of microtubule disassembly thus remains unclear. Here, label-free optical microscopy capable of selective imaging of the transient structural changes of protofilaments at the tip of a disassembling microtubule is introduced. Upon induced disassembly, the transition of ordered protofilaments into a disordered conformation is resolved at the tip of the microtubule. Imaging the unbinding of individual tubulin oligomers from the microtubule tip reveals transient pauses and relapses in the disassembly, concurrent with increased organization of protofilament segments at the microtubule tip. These findings show that microtubule disassembly is a discrete process and suggest a stochastic mechanism of switching from the disassembly to the assembly phase.
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Affiliation(s)
- Milan Vala
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Łukasz Bujak
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Antonio García Marín
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Kristýna Holanová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
| | - Verena Henrichs
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Zdeněk Lánský
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 182 51, Czech Republic
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Jékely G. The chemical brain hypothesis for the origin of nervous systems. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190761. [PMID: 33550946 PMCID: PMC7935135 DOI: 10.1098/rstb.2019.0761] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
In nervous systems, there are two main modes of transmission for the propagation of activity between cells. Synaptic transmission relies on close contact at chemical or electrical synapses while volume transmission is mediated by diffusible chemical signals and does not require direct contact. It is possible to wire complex neuronal networks by both chemical and synaptic transmission. Both types of networks are ubiquitous in nervous systems, leading to the question which of the two appeared first in evolution. This paper explores a scenario where chemically organized cellular networks appeared before synapses in evolution, a possibility supported by the presence of complex peptidergic signalling in all animals except sponges. Small peptides are ideally suited to link up cells into chemical networks. They have unlimited diversity, high diffusivity and high copy numbers derived from repetitive precursors. But chemical signalling is diffusion limited and becomes inefficient in larger bodies. To overcome this, peptidergic cells may have developed projections and formed synaptically connected networks tiling body surfaces and displaying synchronized activity with pulsatile peptide release. The advent of circulatory systems and neurohemal organs further reduced the constraint imposed on chemical signalling by diffusion. This could have contributed to the explosive radiation of peptidergic signalling systems in stem bilaterians. Neurosecretory centres in extant nervous systems are still predominantly chemically wired and coexist with the synaptic brain. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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10
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Evaluation of kinetics and thermodynamics of interaction between immobilized SARS-CoV-2 nucleoprotein and specific antibodies by total internal reflection ellipsometry. J Colloid Interface Sci 2021; 594:195-203. [PMID: 33761394 PMCID: PMC7943374 DOI: 10.1016/j.jcis.2021.02.100] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
During the pandemic, different methods for SARS-CoV-2 detection and COVID-19 diagnostics were developed, including antibody and antigen tests. For a better understanding of the interaction mechanism between SARS-CoV-2 virus proteins and specific antibodies, total internal reflection ellipsometry based evaluation of the interaction between SARS-CoV-2 nucleoprotein (SCoV2-rN) and anti-SCoV2-rN antibodies was performed. Results show that the appropriate mathematical model, which takes into account the formation of an intermediate complex, can be applied for the evaluation of SCoV2-rN/anti-SCoV2-rN complex formation kinetics. The calculated steric factor indicated that SCoV2-rN/anti-SCoV2-rN complex formation has very strict steric requirements. Estimated Gibbs free energy (ΔGAssoc) for SCoV-rN and anti-SCoV-rN binding was determined as −34 kJ/mol. The reported findings are useful for the design of new analytical systems for the determination of anti-SCoV2-rN antibodies and for the development of new anti-SARS-CoV-2 medications.
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11
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Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo. J Mol Biol 2021; 433:166898. [PMID: 33647289 DOI: 10.1016/j.jmb.2021.166898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The crowded cellular milieu affect molecular diffusion through hard (occluded space) and soft (weak, non-specific) interactions. Multiple methods have been developed to measure diffusion coefficients at physiological protein concentrations within cells, each with its limitations. Here, we show that Line-FRAP, combined with rigours data analysis, is able to determine diffusion coefficients in a variety of environments, from in vitro to in vivo. The use of Line mode greatly improves time resolution of FRAP data acquisition, from 20-100 Hz in the classical mode to 800 Hz in the line mode. This improves data analysis, as intensity and radius of the bleach at the first post-bleach frame is critical. We evaluated the method on different proteins labelled chemically or fused to YFP in a wide range of environments. The diffusion coefficients measured in HeLa and in E. coli were ~2.5-fold and 15-fold slower than in buffer, and were comparable to previously published data. Increasing the osmotic pressure on E. coli further decreases diffusion, to the point at which proteins virtually stop moving. The method presented here, which requires a confocal microscope equipped with dual scanners, can be applied to study a large range of molecules with different sizes, and provides robust results in a wide range of environments and protein concentrations for fast diffusing molecules.
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12
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Hegde O, Kabi P, Basu S. Enhancement of mixing in a viscous, non-volatile droplet using a contact-free vapor-mediated interaction. Phys Chem Chem Phys 2020; 22:14570-14578. [PMID: 32596709 DOI: 10.1039/d0cp01004a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mixing at small fluidic length scales is especially challenging in viscous and non-volatile droplets frequently encountered in bio-chemical assays. In situ methods of mixing, which depend on diffusion or evaporation-driven capillary flow, are typically slow and inefficient, while thermal or electro-capillary methods that are either complicated to implement or may cause sample denaturing. This article demonstrates an enhanced mixing timescale in a sessile droplet of glycerol by simply introducing a droplet of ethanol in its near vicinity. The fast evaporation of ethanol introduces molecules in the proximity of the glycerol droplet, which are preferentially adsorbed (more on the side closer to ethanol) creating a gradient of surface tension driving the Marangoni convection in the droplet. We conclusively show that for the given volume of the droplet, the mixing time reduces by ∼10 hours due to the vapour-mediated Marangoni convection. Simple scaling arguments are used to predict the enhancement of the mixing timescale. Experimental evidence obtained from fluorescence imaging is used to quantify mixing and validate the analytical results. This is the first proof of concept of enhanced mixing in a viscous, sessile droplet using the vapour mediation technique.
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Affiliation(s)
- Omkar Hegde
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore-560012, India.
| | - Prasenjit Kabi
- Interdisciplinary Centre for Energy Research, Indian Institute of Science, Bangalore-560012, India
| | - Saptarshi Basu
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore-560012, India.
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13
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Spiropyran labeling for sensitive probing of protein diffusion by the transient grating method. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Kalra AP, Kar P, Preto J, Rezania V, Dogariu A, Lewis JD, Tuszynski JA, Shankar K. Behavior of α, β tubulin in DMSO-containing electrolytes. NANOSCALE ADVANCES 2019; 1:3364-3371. [PMID: 36133560 PMCID: PMC9418024 DOI: 10.1039/c9na00035f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 06/18/2019] [Indexed: 06/11/2023]
Abstract
α, β-tubulin is a cytoskeletal protein that forms cylindrical structures termed microtubules, which are crucial to the cell for a variety of roles. Microtubules are frequently modelled as one-dimensional bionanowires that act as ion transporters in the cell. In this work, we used dynamic light scattering (DLS) to measure the hydrodynamic diameter of tubulin in the presence of a polar aprotic co-solvent. We found that the hydrodynamic diameter increased with increasing DMSO volume fraction, almost doubling at 20% DMSO. To evaluate if this was due to an enlarged solvation shell, we performed reference interaction site model (RISM) simulations and found that the extent of solvation was unchanged. Using fluorescence microscopy, we then showed that tubulin was polymerization competent in the presence of colchicine, and thus inferred the presence of oligomers in the presence of DMSO, which points to its mechanism of action as a microtubule polymerization enhancing agent. Tubulin oligomers are known to form when microtubules depolymerize and are controversially implicated in microtubule polymerization. We show that DLS may be used to monitor early-state microtubule polymerization and is a viable alternative to fluorescence and electron microscopy-based methods. Our findings showing that DMSO causes tubulin oligomerization are thus of critical importance, both for creating bio-inspired nanotechnology and determining its biophysical roles in the cell.
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Affiliation(s)
- Aarat P Kalra
- Department of Physics, University of Alberta 11335 Saskatchewan Dr NW Edmonton Alberta T6G 2M9 Canada
| | - Piyush Kar
- Department of Electrical and Computer Engineering, University of Alberta 9107-116 St Edmonton Alberta T6G 2V4 Canada
| | - Jordane Preto
- Department of Physics, University of Alberta 11335 Saskatchewan Dr NW Edmonton Alberta T6G 2M9 Canada
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University Edmonton Alberta T5J 4S2 Canada
| | - Aristide Dogariu
- CREOL, The College of Optics and Photonics, University of Central Florida Orlando FL 32816 USA
| | - John D Lewis
- Department of Oncology, University of Alberta Edmonton Alberta T6G 1Z2 Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta 11335 Saskatchewan Dr NW Edmonton Alberta T6G 2M9 Canada
- Department of Oncology, University of Alberta Edmonton Alberta T6G 1Z2 Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta 9107-116 St Edmonton Alberta T6G 2V4 Canada
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15
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Chafai DE, Sulimenko V, Havelka D, Kubínová L, Dráber P, Cifra M. Reversible and Irreversible Modulation of Tubulin Self-Assembly by Intense Nanosecond Pulsed Electric Fields. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1903636. [PMID: 31408579 DOI: 10.1002/adma.201903636] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/26/2019] [Indexed: 05/21/2023]
Abstract
Tubulin self-assembly into microtubules is a fascinating natural phenomenon. Its importance is not just crucial for functional and structural biological processes, but it also serves as an inspiration for synthetic nanomaterial innovations. The modulation of the tubulin self-assembly process without introducing additional chemical inhibitors/promoters or stabilizers has remained an elusive process. This work reports a versatile and vigorous strategy for controlling tubulin self-assembly by nanosecond electropulses (nsEPs). The polymerization assessed by turbidimetry is dependent on nsEPs dosage. The kinetics of microtubules formation is tightly linked to the nsEPs effects on structural properties of tubulin, and tubulin-solvent interface, assessed by autofluorescence, and the zeta potential. Moreover, the overall size of tubulin assessed by dynamic light scattering is affected as well. Additionally, atomic force microscopy imaging reveals the formation of different assemblies reflecting applied nsEPs. It is suggested that changes in C-terminal modification states alter tubulin polymerization-competent conformations. Although the assembled tubulin preserve their integral structure, they might exhibit a broad range of new properties important for their functions. Thus, these transient conformation changes of tubulin and their collective properties can result in new applications.
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Affiliation(s)
- Djamel Eddine Chafai
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
| | - Vadym Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Daniel Havelka
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
| | - Lucie Kubínová
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Michal Cifra
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
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16
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Schummel PH, Anders C, Jaworek MW, Winter R. Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer. Chemphyschem 2019; 20:1098-1109. [PMID: 30829441 DOI: 10.1002/cphc.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Indexed: 11/09/2022]
Abstract
Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.
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Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Christian Anders
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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17
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Yu M, Silva TC, van Opstal A, Romeijn S, Every HA, Jiskoot W, Witkamp GJ, Ottens M. The Investigation of Protein Diffusion via H-Cell Microfluidics. Biophys J 2019; 116:595-609. [PMID: 30736981 PMCID: PMC6383004 DOI: 10.1016/j.bpj.2019.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/30/2018] [Accepted: 01/02/2019] [Indexed: 11/26/2022] Open
Abstract
In this study, we developed a microfluidics method, using a so-called H-cell microfluidics device, for the determination of protein diffusion coefficients at different concentrations, pHs, ionic strengths, and solvent viscosities. Protein transfer takes place in the H-cell channels between two laminarly flowing streams with each containing a different initial protein concentration. The protein diffusion coefficients are calculated based on the measured protein mass transfer, the channel dimensions, and the contact time between the two streams. The diffusion rates of lysozyme, cytochrome c, myoglobin, ovalbumin, bovine serum albumin, and etanercept were investigated. The accuracy of the presented methodology was demonstrated by comparing the measured diffusion coefficients with literature values measured under similar solvent conditions using other techniques. At low pH and ionic strength, the measured lysozyme diffusion coefficient increased with the protein concentration gradient, suggesting stronger and more frequent intermolecular interactions. At comparable concentration gradients, the measured lysozyme diffusion coefficient decreased drastically as a function of increasing ionic strength (from zero onwards) and increasing medium viscosity. Additionally, a particle tracing numerical simulation was performed to achieve a better understanding of the macromolecular displacement in the H-cell microchannels. It was found that particle transfer between the two channels tends to speed up at low ionic strength and high concentration gradient. This confirms the corresponding experimental observation of protein diffusion measured via the H-cell microfluidics.
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Affiliation(s)
- Miao Yu
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - Andries van Opstal
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Stefan Romeijn
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Hayley A Every
- FeyeCon Development & Implementation, Weesp, the Netherlands
| | - Wim Jiskoot
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Geert-Jan Witkamp
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, Thuwal, Saudi Arabia
| | - Marcel Ottens
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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18
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Koczian F, Nagło O, Vomacka J, Vick B, Servatius P, Zisis T, Hettich B, Kazmaier U, Sieber SA, Jeremias I, Zahler S, Braig S. Targeting the endoplasmic reticulum-mitochondria interface sensitizes leukemia cells to cytostatics. Haematologica 2018; 104:546-555. [PMID: 30309851 PMCID: PMC6395311 DOI: 10.3324/haematol.2018.197368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Combination chemotherapy has proven to be a favorable strategy to treat acute leukemia. However, the introduction of novel compounds remains challenging and is hindered by a lack of understanding of their mechanistic interactions with established drugs. In the present study, we demonstrate a highly increased response of various acute leukemia cell lines, drug-resistant cells and patient-derived xenograft cells by combining the recently introduced protein disulfide isomerase inhibitor PS89 with cytostatics. In leukemic cells, a proteomics-based target fishing approach revealed that PS89 affects a whole network of endoplasmic reticulum homeostasis proteins. We elucidate that the strong induction of apoptosis in combination with cytostatics is orchestrated by the PS89 target B-cell receptor-associated protein 31, which transduces apoptosis signals at the endoplasmic reticulum -mitochondria interface. Activation of caspase-8 and cleavage of B-cell receptor-associated protein 31 stimulate a pro-apoptotic crosstalk including release of calcium from the endoplasmic reticulum and an increase in the levels of reactive oxygen species resulting in amplification of mitochondrial apoptosis. The findings of this study promote PS89 as a novel chemosensitizing agent for the treatment of acute leukemia and uncovers that targeting the endoplasmic reticulum - mitochondrial network of cell death is a promising approach in combination therapy.
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Affiliation(s)
- Fabian Koczian
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Olga Nagło
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Jan Vomacka
- Department of Chemistry, Technical University of Munich, Garching
| | - Binje Vick
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health, Munich
| | - Phil Servatius
- Institute of Organic Chemistry, Saarland University, Saarbrücken, Germany
| | - Themistoklis Zisis
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Britta Hettich
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Uli Kazmaier
- Institute of Organic Chemistry, Saarland University, Saarbrücken, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technical University of Munich, Garching
| | - Irmela Jeremias
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health, Munich
| | - Stefan Zahler
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
| | - Simone Braig
- Department of Pharmaceutical Biology, Ludwig Maximilian University of Munich
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19
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Hodges C, Kafle RP, Hoff JD, Meiners JC. Fluorescence Correlation Spectroscopy with Photobleaching Correction in Slowly Diffusing Systems. J Fluoresc 2018; 28:505-511. [PMID: 29368157 DOI: 10.1007/s10895-018-2210-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/15/2018] [Indexed: 12/23/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful tool to quantitatively study the diffusion of fluorescently labeled molecules. It allows in principle important questions of macromolecular transport and supramolecular aggregation in living cells to be addressed. However, the crowded environment inside the cells slows diffusion and limits the reservoir of labeled molecules, causing artifacts that arise especially from photobleaching and limit the utility of FCS in these applications. We present a method to compute the time correlation function from weighted photon arrival times, which compensates computationally during the data analysis for the effect of photobleaching. We demonstrate the performance of this method using numerical simulations and experimental data from model solutions. Using this technique, we obtain correlation functions in which the effect of photobleaching has been removed and in turn recover quantitatively accurate mean-square displacements of the fluorophores, especially when deviations from an ideal Gaussian excitation volume are accounted for by using a reference calibration correlation function. This allows quantitative FCS studies of transport processes in challenging environments with substantial photobleaching like in living cells in the future.
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Affiliation(s)
- Cameron Hodges
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA
| | - Rudra P Kafle
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA.,Department of Physics, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA, 01609-2280, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA
| | - Jens-Christian Meiners
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA. .,Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI, 48109-1120, USA.
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20
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Sáez-Calvo G, Sharma A, Balaguer FDA, Barasoain I, Rodríguez-Salarichs J, Olieric N, Muñoz-Hernández H, Berbís MÁ, Wendeborn S, Peñalva MA, Matesanz R, Canales Á, Prota AE, Jímenez-Barbero J, Andreu JM, Lamberth C, Steinmetz MO, Díaz JF. Triazolopyrimidines Are Microtubule-Stabilizing Agents that Bind the Vinca Inhibitor Site of Tubulin. Cell Chem Biol 2017; 24:737-750.e6. [DOI: 10.1016/j.chembiol.2017.05.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/29/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
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21
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Goulet DR, Zwolak A, Chiu ML, Nath A, Atkins WM. Diffusion of Soluble Aggregates of THIOMABs and Bispecific Antibodies in Serum. Biochemistry 2017; 56:2251-2260. [PMID: 28394577 DOI: 10.1021/acs.biochem.6b01097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Submicrometer aggregates are frequently present at low levels in antibody-based therapeutics. Although intuition suggests that the fraction of the aggregate or the size of the aggregate present might correlate with deleterious clinical properties or formulation difficulties, it has been challenging to demonstrate which aggregate states, if any, trigger specific biological effects. One source of uncertainty about the putative linkage between aggregation and safety or efficacy lies in the likelihood that noncovalent aggregation differs in ideal buffers versus in serum and biological tissues; self-association or association with other proteins may vary widely with environment. Therefore, methods for monitoring aggregation and aggregate behavior in biologically relevant matrices could provide a tool for better predicting aggregate-dependent clinical outcomes and provide a basis for antibody engineering prior to clinical studies. Here, we generate models for soluble aggregates of THIOMABs and a bispecific antibody (bsAb) of defined size and exploit fluorescence correlation spectroscopy to monitor their diffusion properties in serum and viscosity-matched buffers. The monomers, dimers, and trimers of both THIOMABs and a bsAb reveal a modest increase in diffusion time in serum greater than expected for an increase in viscosity alone. A mixture of larger aggregates containing mostly bsAb pentamers exhibits a marked increase in diffusion time in serum and much greater intrasample variability, consistent with significant aggregation or interactions with serum components. The results indicate that small aggregates of several IgG platforms are not likely to aggregate with serum components, but nanometer-scale aggregates larger than trimers can interact with the serum in an Ab-dependent manner.
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Affiliation(s)
- Dennis R Goulet
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
| | - Adam Zwolak
- Biologics Research, Janssen Research & Development, LLC , Spring House, Pennsylvania 19477, United States
| | - Mark L Chiu
- Biologics Research, Janssen Research & Development, LLC , Spring House, Pennsylvania 19477, United States
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
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22
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Carbonaro M, Di Venere A, Filabozzi A, Maselli P, Minicozzi V, Morante S, Nicolai E, Nucara A, Placidi E, Stellato F. Role of dietary antioxidant (−)-epicatechin in the development of β-lactoglobulin fibrils. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:766-72. [DOI: 10.1016/j.bbapap.2016.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/04/2016] [Accepted: 03/28/2016] [Indexed: 01/03/2023]
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23
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology. PLoS Biol 2015; 13:e1002213. [PMID: 26271032 PMCID: PMC4535883 DOI: 10.1371/journal.pbio.1002213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/26/2015] [Indexed: 11/24/2022] Open
Abstract
Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.
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Affiliation(s)
- Marcel Ander
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
| | | | - Karim Fahmy
- Division of Biophysics, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Biotechnology Center, TU Dresden, Dresden, Germany
| | - Erik Schäffer
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), Universität Tübingen, Tübingen, Germany
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24
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Shi C, Channels WE, Zheng Y, Iglesias PA. A computational model for the formation of lamin-B mitotic spindle envelope and matrix. Interface Focus 2014; 4:20130063. [PMID: 24904732 DOI: 10.1098/rsfs.2013.0063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent reports show that, after nuclear envelope breakdown, lamin-B, a component of the nuclear lamina in interphase, localizes around the mitotic spindle as a membranous network. How this process occurs, however, and how it influences mitotic spindle morphogenesis is unclear. Here, we develop a computational model based on a continuum description to represent the abundance and location of various molecular species involved during mitosis, and use the model to test a number of hypotheses regarding the formation of the mitotic matrix. Our model illustrates that freely diffusible nuclear proteins can be captured and transported to the spindle poles by minus-end-directed microtubule (MT) motors. Moreover, simulations show that these proteins can be used to build a shell-like region that envelopes the mitotic spindle, which helps to improve the focusing of the mitotic spindle by spatially restricting MT polymerization and limiting the effective diffusion of the free MTs. Simulations also confirm that spatially dependent regulation of the spindle network through the Ran system improves spindle focusing and morphology. Our results agree with experimental observations that lamin-B reorganizes around the spindle and helps to maintain spindle morphology.
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Affiliation(s)
- Changji Shi
- Department of Electrical and Computer Engineering , The Johns Hopkins University , 3400 North Charles Street, Baltimore, MD 21218 , USA
| | - Wilbur E Channels
- Department of Electrical and Computer Engineering , The Johns Hopkins University , 3400 North Charles Street, Baltimore, MD 21218 , USA
| | - Yixian Zheng
- Department of Embryology , Carnegie Institution of Washington , 3520 San Martin Drive, Baltimore, MD 21218 , USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering , The Johns Hopkins University , 3400 North Charles Street, Baltimore, MD 21218 , USA
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25
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Melo AM, Prieto M, Coutinho A. Quantifying lipid-protein interaction by fluorescence correlation spectroscopy (FCS). Methods Mol Biol 2014; 1076:575-95. [PMID: 24108645 DOI: 10.1007/978-1-62703-649-8_26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful method to investigate molecular interactions based on the variation of diffusion properties at the single-molecule level. This technique allows studying quantitatively the interaction of fluorescently labeled proteins/peptides with lipid vesicles. Here, we describe how to acquire and analyze FCS partition data in order to accurately determine the protein/peptide partition coefficients between the aqueous and lipid phases. It is shown that the recovery of unbiased partition coefficients from FCS partition curves (fractional amplitude of the bound species versus lipid concentration) requires considering explicitly the Poissonian loading of the lipid vesicles with the fluorescently labeled protein in order to account for the variable liposome brightness in each sample. Additionally, the impact of a trace amount of a fluorescent non-binding component on the partition curves determined by FCS is also discussed.
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Affiliation(s)
- Ana M Melo
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade Técnica de Lisboa, Lisbon, Portugal
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26
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Hjorth JJJ, van Pelt J, Mansvelder HD, van Ooyen A. Competitive dynamics during resource-driven neurite outgrowth. PLoS One 2014; 9:e86741. [PMID: 24498280 PMCID: PMC3911915 DOI: 10.1371/journal.pone.0086741] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/17/2013] [Indexed: 11/18/2022] Open
Abstract
Neurons form networks by growing out neurites that synaptically connect to other neurons. During this process, neurites develop complex branched trees. Interestingly, the outgrowth of neurite branches is often accompanied by the simultaneous withdrawal of other branches belonging to the same tree. This apparent competitive outgrowth between branches of the same neuron is relevant for the formation of synaptic connectivity, but the underlying mechanisms are unknown. An essential component of neurites is the cytoskeleton of microtubules, long polymers of tubulin dimers running throughout the entire neurite. To investigate whether competition between neurites can emerge from the dynamics of a resource such as tubulin, we developed a multi-compartmental model of neurite growth. In the model, tubulin is produced in the soma and transported by diffusion and active transport to the growth cones at the tip of the neurites, where it is assembled into microtubules to elongate the neurite. Just as in experimental studies, we find that the outgrowth of a neurite branch can lead to the simultaneous retraction of its neighboring branches. We show that these competitive interactions occur in simple neurite morphologies as well as in complex neurite arborizations and that in developing neurons competition for a growth resource such as tubulin can account for the differential outgrowth of neurite branches. The model predicts that competition between neurite branches decreases with path distance between growth cones, increases with path distance from growth cone to soma, and decreases with a higher rate of active transport. Together, our results suggest that competition between outgrowing neurites can already emerge from relatively simple and basic dynamics of a growth resource. Our findings point to the need to test the model predictions and to determine, by monitoring tubulin concentrations in outgrowing neurons, whether tubulin is the resource for which neurites compete.
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Affiliation(s)
- J J Johannes Hjorth
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jaap van Pelt
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
| | - Arjen van Ooyen
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
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27
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Cell motility and drug gradients in the emergence of resistance to chemotherapy. Proc Natl Acad Sci U S A 2013; 110:16103-8. [PMID: 24046372 DOI: 10.1073/pnas.1314385110] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The emergence of resistance to chemotherapy by cancer cells, when combined with metastasis, is the primary driver of mortality in cancer and has proven to be refractory to many efforts. Theory and computer modeling suggest that the rate of emergence of resistance is driven by the strong selective pressure of mutagenic chemotherapy and enhanced by the motility of mutant cells in a chemotherapy gradient to areas of higher drug concentration and lower population competition. To test these models, we constructed a synthetic microecology which superposed a mutagenic doxorubicin gradient across a population of motile, metastatic breast cancer cells (MDA-MB-231). We observed the emergence of MDA-MB-231 cancer cells capable of proliferation at 200 nM doxorubicin in this complex microecology. Individual cell tracking showed both movement of the MDA-MB-231 cancer cells toward higher drug concentrations and proliferation of the cells at the highest doxorubicin concentrations within 72 h, showing the importance of both motility and drug gradients in the emergence of resistance.
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28
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Affiliation(s)
- Yves Engelborghs
- University of Leuven, Biomolecular Dynamics, Celestijnenlaan, Belgium.
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29
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Nouar R, Devred F, Breuzard G, Peyrot V. FRET and FRAP imaging: approaches to characterise tau and stathmin interactions with microtubules in cells. Biol Cell 2013; 105:149-61. [PMID: 23312015 DOI: 10.1111/boc.201200060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/09/2013] [Indexed: 12/13/2022]
Abstract
Microtubules (MTs) are involved in many crucial processes such as cell morphogenesis, mitosis and motility. These dynamic structures resulting from the complex assembly of tubulin are tightly regulated by stabilising MT-associated proteins (MAPs) such as tau and destabilising proteins, notably stathmin. Because of their key role, these MAPs and their interactions have been extensively studied using biochemical and biophysical approaches, particularly in vitro. Nevertheless, numerous questions remain unanswered and the mechanisms of interaction between MT and these proteins are still unclear in cells. Techniques coupling cell imaging and fluorescence methods, such as Förster resonance energy transfer and fluorescence recovery after photobleaching, are excellent tools to study these interactions in situ. After describing these methods, we will present emblematic data from the literature and unpublished experimental results from our laboratory concerning the interactions between MTs, tau and stathmin in cells.
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Affiliation(s)
- Roqiya Nouar
- INSERM UMR 911, Aix-Marseille Université, CRO2, 13385, Marseille, France
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30
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Chakraborty M, Kuriata A, Nathan Henderson J, Salvucci M, Wachter R, Levitus M. Protein oligomerization monitored by fluorescence fluctuation spectroscopy: self-assembly of rubisco activase. Biophys J 2012; 103:949-58. [PMID: 23009844 PMCID: PMC3433602 DOI: 10.1016/j.bpj.2012.07.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/18/2012] [Accepted: 07/23/2012] [Indexed: 12/22/2022] Open
Abstract
A methodology is presented to characterize complex protein assembly pathways by fluorescence correlation spectroscopy. We have derived the total autocorrelation function describing the behavior of mixtures of labeled and unlabeled protein under equilibrium conditions. Our modeling approach allows us to quantitatively consider the relevance of any proposed intermediate form, and K(d) values can be estimated even when several oligomeric species coexist. We have tested this method on the AAA+ ATPase Rubisco activase (Rca). Rca self-association regulates the CO(2) fixing activity of the enzyme Rubisco, directly affecting biomass accumulation in higher plants. However, the elucidation of its assembly pathway has remained challenging, precluding a detailed mechanistic investigation. Here, we present the first, to our knowledge, thermodynamic characterization of oligomeric states of cotton β-Rca complexed with Mg·ADP. We find that the monomer is the dominating species below 0.5 micromolar. The most plausible model supports dissociation constants of ∼4, 1, and 1 micromolar for the monomer-dimer, dimer-tetramer, and tetramer-hexamer equilibria, in line with the coexistence of four different oligomeric forms under typical assay conditions. Large aggregates become dominant above 40 micromolar, with continued assembly at even higher concentrations. We propose that under some conditions, ADP-bound Rca self-associates by forming spiral arrangements that grow along the helical axis. Other models such as the stacking of closed hexameric rings are also discussed.
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Affiliation(s)
- Manas Chakraborty
- Department of Chemistry and Biochemistry and the Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Agnieszka M. Kuriata
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - J. Nathan Henderson
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Michael E. Salvucci
- Arid-Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, Arizona
| | - Rebekka M. Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Marcia Levitus
- Department of Chemistry and Biochemistry and the Biodesign Institute, Arizona State University, Tempe, Arizona
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31
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Paredes JM, Casares S, Ruedas-Rama MJ, Fernandez E, Castello F, Varela L, Orte A. Early amyloidogenic oligomerization studied through fluorescence lifetime correlation spectroscopy. Int J Mol Sci 2012; 13:9400-9418. [PMID: 22949804 PMCID: PMC3431802 DOI: 10.3390/ijms13089400] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/13/2012] [Accepted: 07/19/2012] [Indexed: 12/20/2022] Open
Abstract
Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored the initial stages of amyloidogenic aggregation by employing fluorescence lifetime correlation spectroscopy (FLCS), an advanced modification of conventional fluorescence correlation spectroscopy (FCS) that utilizes time-resolved information. FLCS provides size distributions and kinetics for the oligomer growth of the SH3 domain of α-spectrin, whose N47A mutant forms amyloid fibrils at pH 3.2 and 37 °C in the presence of salt. The combination of FCS with additional fluorescence lifetime information provides an exciting approach to focus on the initial aggregation stages, allowing a better understanding of the fibrillization process, by providing multidimensional information, valuable in combination with other conventional methodologies.
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Affiliation(s)
- Jose M. Paredes
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Salvador Casares
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Maria J. Ruedas-Rama
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Elena Fernandez
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Fabio Castello
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
| | - Lorena Varela
- Department of Physical Chemistry, Faculty of Sciences, Campus Fuentenueva, Granada, 18071, Spain; E-Mails: (S.C.); (E.F.); (L.V.A.)
| | - Angel Orte
- Department of Physical Chemistry, Faculty of Pharmacy, Campus Cartuja, Granada, 18071, Spain; E-Mails: (J.M.P.); (M.J.R.-R.); (F.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-958-243825; Fax: +34-958-244090
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32
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Hepburn I, Chen W, Wils S, De Schutter E. STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC SYSTEMS BIOLOGY 2012; 6:36. [PMID: 22574658 PMCID: PMC3472240 DOI: 10.1186/1752-0509-6-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 05/10/2012] [Indexed: 11/13/2022]
Abstract
Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/
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Affiliation(s)
- Iain Hepburn
- Theoretical Neurobiology, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, Wilrijk 2610, Belgium.
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33
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Nath S, Deng M, Engelborghs Y. Fluorescence correlation spectroscopy to determine the diffusion coefficient of α-synuclein and follow early oligomer formation. Methods Mol Biol 2012; 895:499-506. [PMID: 22760336 DOI: 10.1007/978-1-61779-927-3_29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) can be used to determine the diffusion coefficient of fluorescently labeled α-synuclein. It is a technique based on the use of a confocal microscope. By applying FCS in a combination of short sampling times and repeated measurements, the disappearance of individual α-synuclein molecules (called monomers) and the formation of oligomers can be characterized during the early aggregation process.
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Affiliation(s)
- Sangeeta Nath
- Laboratory of Biomolecular Dynamics, University of Leuven, Leuven, Belgium
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34
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Melo AM, Prieto M, Coutinho A. The effect of variable liposome brightness on quantifying lipid–protein interactions using fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2559-68. [DOI: 10.1016/j.bbamem.2011.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/01/2011] [Accepted: 06/01/2011] [Indexed: 11/17/2022]
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35
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Badali D, Gradinaru CC. The effect of Brownian motion of fluorescent probes on measuring nanoscale distances by Förster resonance energy transfer. J Chem Phys 2011; 134:225102. [PMID: 21682537 DOI: 10.1063/1.3598109] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a powerful optical technique to determine intra-molecular distances. However, the dye rotational motion and the linker flexibility complicate the relationship between the measured energy transfer efficiency and the distance between the anchoring points of the dyes. In this study, we present a simple model that describes the linker and dye dynamics as diffusion on a sphere. Single-pair energy transfer was treated in the weak excitation limit, photon statistics and scaffold flexibility were ignored, and different time-averaging regimes were considered. Despite the approximations, our model provides new insights for experimental designs and results interpretation in single-molecule FRET. Monte Carlo simulations produced distributions of the inter-dye distance, the dipole orientation factor, κ(2), and the transfer efficiency, E, which were in perfect agreement with independently derived theoretical functions. Contrary to common perceptions, our data show that longer linkers will actually restrict the motion of dye dipoles and hence worsen the isotropic 2∕3 approximation of κ(2). It is also found that the thermal motions of the dye-linker system cause fast and large efficiency fluctuations, as shown by the simulated FRET time-trajectories binned on a microsecond time scale. A fundamental resolution limit of single-molecule FRET measurements emerges around 1-10 μs, which should be considered for the interpretation of data recorded on such fast time scales.
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Affiliation(s)
- Daniel Badali
- Department of Physics and Institute for Optical Sciences, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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36
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Hunke C, Antosch M, Müller V, Grüber G. Binding of subunit E into the A-B interface of the A(1)A(O) ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2111-8. [PMID: 21669184 DOI: 10.1016/j.bbamem.2011.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 11/17/2022]
Abstract
Two of the distinct diversities of the engines A(1)A(O) ATP synthase and F(1)F(O) ATP synthase are the existence of two peripheral stalks and the 24kDa stalk subunit E inside the A(1)A(O) ATP synthase. Crystallographic structures of subunit E have been determined recently, but the epitope(s) and the strength to which this subunit does bind in the enzyme complex are still a puzzle. Using the recombinant A(3)B(3)D complex and the major subunits A and B of the methanogenic A(1)A(O) ATP synthase in combination with fluorescence correlation spectroscopy (FCS) we demonstrate, that the stalk subunit E does bind to the catalytic headpiece formed by the A(3)B(3) hexamer with an affinity (K(d)) of 6.1±0.2μM. FCS experiments with single A and B, respectively, demonstrated unequivocally that subunit E binds stronger to subunit B (K(d)=18.9±3.7μM) than to the catalytic A subunit (K(d)=53.1±4.4). Based on the crystallographic structures of the three subunits A, B and E available, the arrangement of the peripheral stalk subunit E in the A-B interface has been modeled, shining light into the A-B-E assembly of this enzyme.
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Affiliation(s)
- Cornelia Hunke
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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37
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A percolation-like model for simulating inter-cellular diffusion in the context of bystander signalling in tumour. AUSTRALASIAN PHYSICAL & ENGINEERING SCIENCES IN MEDICINE 2010; 34:31-9. [DOI: 10.1007/s13246-010-0048-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 12/15/2010] [Indexed: 11/26/2022]
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38
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Mitsuhashi M, Sakata H, Kinjo M, Yazawa M, Takahashi M. Dynamic assembly properties of nonmuscle myosin II isoforms revealed by combination of fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. J Biochem 2010; 149:253-63. [PMID: 21106542 DOI: 10.1093/jb/mvq134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Myosin II molecules assemble into filaments through their C-terminal rod region, and are responsible for several cellular motile activities. Three isoforms of nonmuscle myosin II (IIA, IIB and IIC) are expressed in mammalian cells. However, little is known regarding the isoform composition in filaments. To obtain new insight into the assembly properties of myosin II isoforms, especially regarding the isoform composition in filaments, we performed a combination analysis of fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS), which enables us to acquire information on both the interaction and the size of each molecule simultaneously. Using C-terminal rod fragments of IIA and IIB (ARF296 and BRF305) labelled with different fluorescent probes, we demonstrated that hetero-assemblies were formed from a mixture of ARF296 and BRF305, and that dynamic exchange of rod fragments occurred between preformed homo-assemblies of each isoform in an isoform-independent manner. We also showed that Mts1 (S100A4) specifically stripped ARF296 away from the hetero-assemblies, and consequently, homo-assemblies of BRF305 were formed. These results suggest that IIA and IIB can form hetero-filaments in an isoform-independent manner, and that a factor like Mts1 can remove one isoform from the hetero-filament, resulting in a formation of homo-filaments consisting of another isoform.
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Affiliation(s)
- Mariko Mitsuhashi
- Division of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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39
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The structural parameters for antimicrobial activity, human epithelial cell cytotoxicity and killing mechanism of synthetic monomer and dimer analogues derived from hBD3 C-terminal region. Amino Acids 2010; 40:123-33. [PMID: 20397033 DOI: 10.1007/s00726-010-0565-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
Abstract
Understanding the molecular mechanisms of antimicrobial peptide-membrane interactions is crucial in predicting the design of useful synthetic antimicrobial peptide analogues. Defensins are small (3-5 kDa) cysteine-rich cationic proteins which constitute the front line of host innate immunity. In this study, a series of eight 10 AA C-terminal analogues of hBD3 [sequence: RGRKXXRRKK, X = W, F, Y, V, L, I, H, C(Acm); net charge = +7, coded as W2, F2, Y2, V2, L2, I2, H2, and C2] and covalent V2-dimer [(RGRKVVRR)(2)KK] (18 AA, net charge = +11) were synthesized using solid phase peptide synthesis (SPPS) in Fmoc chemistry. Wild-type hBD3 was used as a control in all analyses. W2, V2, and especially Y2 showed high activity selectively against Gram-negative bacteria Pseudomonas aeruginosa in the concentration range of 4.3-9.7 microM. The covalent dimeric form of V2-monomer, V2-dimer, showed increased antibacterial killing compared to the monomeric form, V2-monomer. Cytotoxicity assays on a human conjunctival epithelial cell line (IOBA-NHC cells) showed that no change in viable cell number 24 h after constant exposure to all the eight peptide analogues even at concentrations up to 200 microg/ml. Fluorescence correlation spectroscopy (FCS) was used to study the interaction of these peptides against POPC vesicles (neutral; mammalian cell membrane mimic) and POPG vesicles (negatively charged; bacterial cell membrane mimic). Using FCS, significant aggregation and some leakage of Rhodamine dye were observed with POPG with Y2, W2 and V2 at the concentration of 5-10 mmicroM and no significant aggregation or disruption of vesicles was observed for all peptide analogues tested against POPC. V2-dimer induced more leakage and aggregation than the monomeric form. Overall, V2-dimer is the most effective antimicrobial peptide, with aggregation of POPG vesicles observed at concentrations as low as 1 microM. The concentration of 5-10 microM for Y2 from FCS correlated with the concentration of 5 microM (6.25 microg/ml), at which Y2 showed a cooperative increase in the activity. This suggests a structural transition of Y2 in the 2.5-5 microM concentration range resulting in the correlated increased antimicrobial activity. These results and the FCS together with previous NMR and molecular dynamics (MD) suggested that the charge density-based binding affinity, stable covalent dimerization, the ability to dimerize or even oligomerize and adopt a well-defined structure are important physicochemical properties distinguishing more effective cationic antimicrobial peptides.
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40
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Nath S, Meuvis J, Hendrix J, Carl SA, Engelborghs Y. Early aggregation steps in alpha-synuclein as measured by FCS and FRET: evidence for a contagious conformational change. Biophys J 2010; 98:1302-11. [PMID: 20371330 PMCID: PMC2849099 DOI: 10.1016/j.bpj.2009.12.4290] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 12/01/2009] [Accepted: 12/02/2009] [Indexed: 11/30/2022] Open
Abstract
The kinetics of aggregation of alpha-synuclein are usually studied by turbidity or Thio-T fluorescence. Here we follow the disappearance of monomers and the formation of early oligomers using fluorescence correlation spectroscopy. Alexa488-labeled A140C-synuclein was used as a fluorescent probe in trace amounts in the presence of excess unlabeled alpha-synuclein. Repeated short measurements produce a distribution of diffusion coefficients. Initially, a sharp peak is obtained corresponding to monomers, followed by a distinct transient population and the gradual formation of broader-sized distributions of higher oligomers. The kinetics of aggregation can be followed by the decreasing number of fast-diffusing species. Both the disappearance of fast-diffusing species and the appearance of turbidity can be fitted to the Finke-Watzky equation, but the apparent rate constants obtained are different. This reflects the fact that the disappearance of fast species occurs largely during the lag phase of turbidity development, due to the limited sensitivity of turbidity to the early aggregation process. The nucleation of the early oligomers is concentration-dependent and accompanied by a conformational change that precedes beta-structure formation, and can be visualized using fluorescence resonance energy transfer between the donor-labeled N-terminus and the acceptor-labeled cysteine in the mutant A140C.
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Affiliation(s)
- Sangeeta Nath
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Jessika Meuvis
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
| | - Shaun A. Carl
- Laboratory of Quantum and Physical Chemistry, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Yves Engelborghs
- Laboratory of Biomolecular Dynamics, Department of Chemistry & BioSCENTer, University of Leuven, Leuven, Belgium
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41
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Blom H, Björk G. Lorentzian spatial intensity distribution in one-photon fluorescence correlation spectroscopy. APPLIED OPTICS 2009; 48:6050-6058. [PMID: 19881673 DOI: 10.1364/ao.48.006050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The theory of autocorrelation-function evaluation in fluorescence correlation spectroscopy is applied to a Lorentzian intensity distribution. An analytical solution to the autocorrelation function for diffusion is deduced for this spatial distribution. Experimental investigation of the distribution is performed using an enlarged detector aperture in a standard confocal setup. The data from the experiment are fitted to the derived autocorrelation function, and a reasonable estimate of the spatial distribution is provided. Estimates are also compared to values computed by molecular detection efficiency simulation. The use of Lorentzian intensity distributions complements conditions where a Gaussian intensity distribution applies, expanding the applicability range of analytical correlation functions.
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Affiliation(s)
- Hans Blom
- Department of Applied Physics, Royal Institute of Technology, AlbaNova/KTH,Roslagstullsbacken 21, 10691 Stockholm, Sweden.
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42
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Hwang H, Park JK. Dynamic Light-Activated Control of Local Chemical Concentration in a Fluid. Anal Chem 2009; 81:5865-70. [DOI: 10.1021/ac901047v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyundoo Hwang
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwanhangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwanhangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
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43
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Sugiki T, Yoshiura C, Kofuku Y, Ueda T, Shimada I, Takahashi H. High-throughput screening of optimal solution conditions for structural biological studies by fluorescence correlation spectroscopy. Protein Sci 2009; 18:1115-20. [PMID: 19388076 PMCID: PMC2771313 DOI: 10.1002/pro.92] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 01/27/2009] [Accepted: 02/02/2009] [Indexed: 11/07/2022]
Abstract
Protein aggregation is an essential molecular event in a wide variety of biological situations, and is a causal factor in several degenerative diseases. The aggregation of proteins also frequently hampers structural biological analyses, such as solution NMR studies. Therefore, precise detection and characterization of protein aggregation are of crucial importance for various research fields. In this study, we demonstrate that fluorescence correlation spectroscopy (FCS) using a single-molecule fluorescence detection system enables the detection of otherwise invisible aggregation of proteins at higher protein concentrations, which are suitable for structural biological experiments, and consumes relatively small amounts of protein over a short measurement time. Furthermore, utilizing FCS, we established a method for high-throughput screening of protein aggregation and optimal solution conditions for structural biological experiments.
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Affiliation(s)
- Toshihiko Sugiki
- Japan Biological Informatics Consortium (JBiC)Aomi, Koto-ku, Tokyo 135-8073, Japan
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, the University of TokyoHongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, the University of TokyoHongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, the University of TokyoHongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)Aomi, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Pharmaceutical Sciences, the University of TokyoHongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideo Takahashi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)Aomi, Koto-ku, Tokyo 135-0064, Japan
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44
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Weidtkamp-Peters S, Felekyan S, Bleckmann A, Simon R, Becker W, Kühnemuth R, Seidel CAM. Multiparameter fluorescence image spectroscopy to study molecular interactions. Photochem Photobiol Sci 2009; 8:470-80. [PMID: 19337660 DOI: 10.1039/b903245m] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiparameter Fluorescence Image Spectroscopy (MFIS) is used to monitor simultaneously a variety of fluorescence parameters in confocal fluorescence microscopy. As the photons are registered one by one, MFIS allows for fully parallel recording of Fluorescence Correlation/Cross Correlation Spectroscopy (FCS/FCCS), fluorescence lifetime and pixel/image information over time periods of hours with picosecond accuracy. The analysis of the pixel fluorescence information in higher-dimensional histograms maximizes the selectivity of fluorescence microscopic methods. Moreover it facilitates a statistically-relevant data analysis of the pixel information which makes an efficient detection of heterogeneities possible. The reliability of MFIS has been demonstrated for molecular interaction studies in different complex environments: (I) detecting the heterogeneity of diffusion properties of the dye Rhodamine 110 in a sepharose bead, (II) Förster Resonance Energy Transfer (FRET) studies in mammalian HEK293 cells, and (III) FRET study of the homodimerisation of the transcription factor BIM1 in plant cells. The multidimensional analysis of correlated changes of several parameters measured by FRET, FCS, fluorescence lifetime and anisotropy increases the robustness of the analysis significantly. The economic use of photon information allows one to keep the expression levels of fluorescent protein-fusion proteins as low as possible (down to the single-molecule level).
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Affiliation(s)
- Stefanie Weidtkamp-Peters
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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Ghosh R, Sharma S, Chattopadhyay K. Effect of Arginine on Protein Aggregation Studied by Fluorescence Correlation Spectroscopy and Other Biophysical Methods. Biochemistry 2009; 48:1135-43. [DOI: 10.1021/bi802065j] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ranendu Ghosh
- Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sunny Sharma
- Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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46
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Mechulam A, Chernov KG, Mucher E, Hamon L, Curmi PA, Pastré D. Polyamine sharing between tubulin dimers favours microtubule nucleation and elongation via facilitated diffusion. PLoS Comput Biol 2009; 5:e1000255. [PMID: 19119409 PMCID: PMC2599886 DOI: 10.1371/journal.pcbi.1000255] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 11/17/2008] [Indexed: 12/18/2022] Open
Abstract
We suggest for the first time that the action of multivalent cations on microtubule dynamics can result from facilitated diffusion of GTP-tubulin to the microtubule ends. Facilitated diffusion can promote microtubule assembly, because, upon encountering a growing nucleus or the microtubule wall, random GTP-tubulin sliding on their surfaces will increase the probability of association to the target sites (nucleation sites or MT ends). This is an original explanation for understanding the apparent discrepancy between the high rate of microtubule elongation and the low rate of tubulin association at the microtubule ends in the viscous cytoplasm. The mechanism of facilitated diffusion requires an attraction force between two tubulins, which can result from the sharing of multivalent counterions. Natural polyamines (putrescine, spermidine, and spermine) are present in all living cells and are potent agents to trigger tubulin self-attraction. By using an analytical model, we analyze the implication of facilitated diffusion mediated by polyamines on nucleation and elongation of microtubules. In vitro experiments using pure tubulin indicate that the promotion of microtubule assembly by polyamines is typical of facilitated diffusion. The results presented here show that polyamines can be of particular importance for the regulation of the microtubule network in vivo and provide the basis for further investigations into the effects of facilitated diffusion on cytoskeleton dynamics.
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Affiliation(s)
- Alain Mechulam
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
| | - Konstantin G. Chernov
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
- Institute of Protein Research, Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Elodie Mucher
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
| | - Loic Hamon
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
| | - Patrick A. Curmi
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules
Normales et Pathologiques, Université Evry-Val d'Essonne,
Evry, France
- INSERM, U829, Evry, France
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Tubulin dimers oligomerize before their incorporation into microtubules. PLoS One 2008; 3:e3821. [PMID: 19043587 PMCID: PMC2584370 DOI: 10.1371/journal.pone.0003821] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 11/06/2008] [Indexed: 01/31/2023] Open
Abstract
In the presence of GTP, purified dimers of α- and β-tubulin will interact longitudinally and laterally to self-assemble into microtubules (MTs). This property provides a powerful in vitro experimental system to describe MT dynamic behavior at the micrometer scale and to study effects and functioning of a large variety of microtubule associated proteins (MAPs). Despite the plethora of such data produced, the molecular mechanisms of MT assembly remain disputed. Electron microscopy (EM) studies suggested that tubulin dimers interact longitudinally to form short oligomers which form a tube by lateral interaction and which contribute to MT elongation. This idea is however challenged: Based on estimated association constants it was proposed that single dimers represent the major fraction of free tubulin. This view was recently supported by measurements suggesting that MTs elongate by addition of single tubulin dimers. To solve this discrepancy, we performed a direct measurement of the longitudinal interaction energy for tubulin dimers. We quantified the size distribution of tubulin oligomers using EM and fluorescence correlation spectroscopy (FCS). From the distribution we derived the longitudinal interaction energy in the presence of GDP and the non-hydrolysable GTP analog GMPCPP. Our data suggest that MT elongation and nucleation involves interactions of short tubulin oligomers rather than dimers. Our approach provides a solid experimental framework to better understand the role of MAPs in MT nucleation and growth.
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Biliverdin reductase is a transporter of haem into the nucleus and is essential for regulation of HO-1 gene expression by haematin. Biochem J 2008; 413:405-16. [PMID: 18412543 DOI: 10.1042/bj20080018] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
hBVR (human biliverdin reductase) is an enzyme that reduces biliverdin (the product of haem oxygenases HO-1 and HO-2 activity) to the antioxidant bilirubin. It also functions as a kinase and as a transcription factor in the MAPK (mitogen-activated protein kinase) signalling cascade. Fluorescence correlation spectroscopy was used to investigate the mobility of hBVR in living cells and its function in the nuclear transport of haematin for induction of HO-1. In transiently transfected HeLa cells only kinase-competent hBVR translocates to the nucleus. A reduced mobility in the nucleus of haematin-treated cells suggests formation of an hBVR-haematin complex and its further association with large nuclear components. The binding of haematin is specific, with the formation of a 1:1 molar complex, and the C-terminal 7-residue fragment KYCCSRK(296) of hBVR contributes to the binding. The following data suggest formation of dynamic complexes of hBVR-haematin with chromatin: (i) the reduction of hBVR mobility in the presence of haematin is greater in heterochromatic regions than in euchromatic domains and (ii) hBVR mobility is not retarded by haematin in nuclear lysates that contain only soluble factors. Moreover, hBVR kinase activity is stimulated in the presence of double-stranded DNA fragments corresponding to HO-1 antioxidant and HREs (hypoxia response elements), as well as by haematin. Experiments with nuclear localization, export signal mutants and si-hBVR [siRNA (small interfering RNA) specific to hBVR] indicate that nuclear localization of hBVR is required for induction of HO-1 by haematin. Because gene regulation is energy-dependent and haematin regulates gene expression, our data suggest that hBVR functions as an essential component of the regulatory mechanisms for haem-responsive transcriptional activation.
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Mamedov TG, Pienaar E, Whitney SE, TerMaat JR, Carvill G, Goliath R, Subramanian A, Viljoen HJ. A fundamental study of the PCR amplification of GC-rich DNA templates. Comput Biol Chem 2008; 32:452-7. [PMID: 18760969 DOI: 10.1016/j.compbiolchem.2008.07.021] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 07/06/2008] [Indexed: 11/18/2022]
Abstract
A theoretical analysis is presented with experimental confirmation to conclusively demonstrate the critical role that annealing plays in efficient PCR amplification of GC-rich templates. The analysis is focused on the annealing of primers at alternative binding sites (competitive annealing) and the main result is a quantitative expression of the efficiency (eta) of annealing as a function of temperature (T(A)), annealing period (t(A)), and template composition. The optimal efficiency lies in a narrow region of T(A) and t(A) for GC-rich templates and a much broader region for normal GC templates. To confirm the theoretical findings, the following genes have been PCR amplified from human cDNA template: ARX and HBB (with 78.72% and 52.99% GC, respectively). Theoretical results are in excellent agreement with the experimental findings. Optimum annealing times for GC-rich genes lie in the range of 3-6s and depend on annealing temperature. Annealing times greater than 10s yield smeared PCR amplified products. The non-GC-rich gene did not exhibit this sensitivity to annealing times. Theory and experimental results show that shorter annealing times are not only sufficient but can actually aid in more efficient PCR amplification of GC-rich templates.
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Affiliation(s)
- T G Mamedov
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0643, USA
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Non-random-coil behavior as a consequence of extensive PPII structure in the denatured state. J Mol Biol 2008; 382:203-12. [PMID: 18644382 DOI: 10.1016/j.jmb.2008.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 06/21/2008] [Accepted: 07/03/2008] [Indexed: 11/21/2022]
Abstract
Unfolded proteins may contain a native or nonnative residual structure, which has important implications for the thermodynamics and kinetics of folding, as well as for misfolding and aggregation diseases. However, it has been universally accepted that residual structure should not affect the global size scaling of the denatured chain, which obeys the statistics of random coil polymers. Here we use a single-molecule optical technique--fluorescence correlation spectroscopy--to probe the denatured state of a set of repeat proteins containing an increasing number of identical domains, from 2 to 20. The availability of this set allows us to obtain the scaling law for the unfolded state of these proteins, which turns out to be unusually compact, strongly deviating from random coil statistics. The origin of this unexpected behavior is traced to the presence of an extensive nonnative polyproline II helical structure, which we localize to specific segments of the polypeptide chain. We show that the experimentally observed effects of polyproline II on the size scaling of the denatured state can be well-described by simple polymer models. Our findings suggest a hitherto unforeseen potential of nonnative structure to induce significant compaction of denatured proteins, significantly affecting folding pathways and kinetics.
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