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Nagahata Y, Kobayashi M, Toda M, Maeda S, Taketsugu T, Komatsuzaki T. An encompassed representation of timescale hierarchies in first-order reaction network. Proc Natl Acad Sci U S A 2024; 121:e2317781121. [PMID: 38758700 PMCID: PMC11126998 DOI: 10.1073/pnas.2317781121] [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: 11/14/2023] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Complex networks are pervasive in various fields such as chemistry, biology, and sociology. In chemistry, first-order reaction networks are represented by a set of first-order differential equations, which can be constructed from the underlying energy landscape. However, as the number of nodes increases, it becomes more challenging to understand complex kinetics across different timescales. Hence, how to construct an interpretable, coarse-graining scheme that preserves the underlying timescales of overall reactions is of crucial importance. Here, we develop a scheme to capture the underlying hierarchical subsets of nodes, and a series of coarse-grained (reduced-dimensional) rate equations between the subsets as a function of time resolution from the original reaction network. Each of the coarse-grained representations guarantees to preserve the underlying slow characteristic timescales in the original network. The crux is the construction of a lumping scheme incorporating a similarity measure in deciphering the underlying timescale hierarchy, which does not rely on the assumption of equilibrium. As an illustrative example, we apply the scheme to four-state Markovian models and Claisen rearrangement of allyl vinyl ether (AVE), and demonstrate that the reduced-dimensional representation accurately reproduces not only the slowest but also the faster timescales of overall reactions although other reduction schemes based on equilibrium assumption well reproduce the slowest timescale but fail to reproduce the second-to-fourth slowest timescales with the same accuracy. Our scheme can be applied not only to the reaction networks but also to networks in other fields, which helps us encompass their hierarchical structures of the complex kinetics over timescales.
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Affiliation(s)
- Yutaka Nagahata
- The Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
| | - Masato Kobayashi
- The Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
| | - Mikito Toda
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
- Faculty Division of Natural Sciences, Nara Women’s University, Nara630-8506, Japan
- Graduate School of Information Science, University of Hyogo, Kobe650-0047, Japan
| | - Satoshi Maeda
- The Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
| | - Tetsuya Taketsugu
- The Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
| | - Tamiki Komatsuzaki
- The Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo001-0020, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita565-0871, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki567-0047, Japan
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2
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Nautiyal A, Thakur M. Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution. ACS OMEGA 2024; 9:12515-12538. [PMID: 38524412 PMCID: PMC10956419 DOI: 10.1021/acsomega.3c09866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.
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Affiliation(s)
- Astha Nautiyal
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Thakur
- Sri
Venkateswara College, Benito Juarez Road, University of Delhi, New Delhi 110021, India
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3
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Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
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Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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4
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Safar M, Saurabh A, Sarkar B, Fazel M, Ishii K, Tahara T, Sgouralis I, Pressé S. Single-photon smFRET. III. Application to pulsed illumination. BIOPHYSICAL REPORTS 2022; 2:100088. [PMID: 36530182 PMCID: PMC9747580 DOI: 10.1016/j.bpr.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single-photon, single-molecule FRET (smFRET) data analysis under pulsed illumination including 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; and 3) taking into account detector noise sources such as cross talk and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion article that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.
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Affiliation(s)
- Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
- School of Molecular Sciences, Arizona State University, Phoenix, Arizona
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5
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Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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6
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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7
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Abstract
Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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8
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Mondal S, Mishra PP. Direct observation of effect of crowding induced macromolecular hydration on molecular breathing in the stem of Fork-DNA by single-molecule FRET microspectroscopy. Int J Biol Macromol 2020; 167:559-569. [PMID: 33278436 DOI: 10.1016/j.ijbiomac.2020.11.197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/15/2022]
Abstract
The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.
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Affiliation(s)
- Soma Mondal
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
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9
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Bera SC, Paul T, Iyengar ANS, Mishra PP. Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction. Faraday Discuss 2019; 207:251-265. [PMID: 29383368 DOI: 10.1039/c7fd00184c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0.270 ± 0.012 to 0.360 ± 0.008). The application of an external force has assisted the conformational transitions to share the unstacked open structure intermediate, with different rate-limiting steps and a huge induced variation in the energy landscape. Furthermore, the associated landscape of the 4WHJ is visualized in terms of rarely interconverting states embedded into the two isoforms by using nonlinear dynamics analysis, which shows that the chaoticity of the system increases at intermediate force (0.4 to 1.6 pN). The identification of chaos in our investigation provides useful information for a comprehensive explanation of the origin of the complex behavior of the system, which effectively helps us to perceive the dynamics of IHF bound 4WHJs under the influence of external force, and also demonstrates the applicability of nonlinear dynamics analysis in the field of biology.
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Affiliation(s)
- Subhas C Bera
- Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
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10
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In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein. Biochim Biophys Acta Gen Subj 2019; 1864:129358. [PMID: 31071411 DOI: 10.1016/j.bbagen.2019.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The structures of proteins are intimately related to their functions. Significant efforts have been dedicated to the structural investigation of proteins, mainly those of purified proteins in in vitro environments. Proteins function in living cells and thus protein structures must be regulated by interactions with various molecules, some of which participate in reaction networks, depending on the states, conditions, or actions of the cell. Therefore, it is very important to understand the structural behavior of proteins in living cells. METHODS Single-molecule Förster resonance energy transfer (smFRET) measurements were conducted using the alternative laser excitation (ALEX) technique. smFRET distributions of cytosolic Rapidly Accelerated Fibrosarcoma (RAF) proteins in living HeLa cells were obtained with exclusion of the negative effects of photobleached fluorophores and incompletely labeled proteins on smFRET. RESULTS smFRET histograms of wildtype (wt) RAF in live cells exhibited two major peaks, whereas that of the S621A mutant, which has been thought to have an expanded structure, was almost single-peaked. A population shift involving the peaks for wt RAF was detected upon epidermal growth factor stimulation. Spontaneous transitions between the conformational states corresponding to the two peaks were also detected using the FRET-two-channel kernel-based density distribution estimator method in comparison to static double-stranded DNA samples. CONCLUSIONS Cytosolic CRAF has at least three conformational states; in addition to the closed and open forms, the fully-open form was distinctly specified. Based on the results, we propose a speculative structural model for CRAF. GENERAL SIGNIFICANCE Structural distribution and changes to proteins in live cells as a result of intracellular interactions were successfully identified. smFRET using ALEX is applicable to any other cytosolic proteins.
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11
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Maeda R, Sato T, Okamoto K, Yanagawa M, Sako Y. Lipid-Protein Interplay in Dimerization of Juxtamembrane Domains of Epidermal Growth Factor Receptor. Biophys J 2019; 114:893-903. [PMID: 29490249 DOI: 10.1016/j.bpj.2017.12.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/17/2017] [Accepted: 12/20/2017] [Indexed: 01/23/2023] Open
Abstract
Transmembrane (TM) helix and juxtamembrane (JM) domains (TM-JM) bridge the extracellular and intracellular domains of single-pass membrane proteins, including epidermal growth factor receptor (EGFR). TM-JM dimerization plays a crucial role in regulation of EGFR kinase activity at the cytoplasmic side. Although the interaction of JM with membrane lipids is thought to be important to turn on EGF signaling, and phosphorylation of Thr654 on JM leads to desensitization, the underlying kinetic mechanisms remain unclear. In particular, how Thr654 phosphorylation regulates EGFR activity is largely unknown. Here, combining single-pair FRET imaging and nanodisc techniques, we showed that phosphatidylinositol 4,5-bis phosphate (PIP2) facilitated JM dimerization effectively. We also found that Thr654 phosphorylation dissociated JM dimers in the membranes containing acidic lipids, suggesting that Thr654 phosphorylation electrostatically prevented the interaction with basic residues in JM and acidic lipids. Based on the single-molecule experiment, we clarified the kinetic pathways of the monomer (inactive state)-to-dimer (active state) transition of JM domains and alteration in the pathways depending on the membrane lipid species and Thr654 phosphorylation.
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Affiliation(s)
- Ryo Maeda
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Japan
| | - Takeshi Sato
- Kyoto Pharmaceutical University, 5, Misasagi-cho, Yamashina-ku, Kyoto-shi, Kyoto, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan
| | - Kenji Okamoto
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Japan
| | | | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Japan.
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12
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Sgouralis I, Madaan S, Djutanta F, Kha R, Hariadi RF, Pressé S. A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer. J Phys Chem B 2019; 123:675-688. [PMID: 30571128 DOI: 10.1021/acs.jpcb.8b09752] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We develop a Bayesian nonparametric framework to analyze single molecule FRET (smFRET) data. This framework, a variation on infinite hidden Markov models, goes beyond traditional hidden Markov analysis, which already treats photon shot noise, in three critical ways: (1) it learns the number of molecular states present in a smFRET time trace (a hallmark of nonparametric approaches), (2) it accounts, simultaneously and self-consistently, for photophysical features of donor and acceptor fluorophores (blinking kinetics, spectral cross-talk, detector quantum efficiency), and (3) it treats background photons. Point 2 is essential in reducing the tendency of nonparametric approaches to overinterpret noisy single molecule time traces and so to estimate states and transition kinetics robust to photophysical artifacts. As a result, with the proposed framework, we obtain accurate estimates of single molecule properties even when the supplied traces are excessively noisy, subject to photoartifacts, and of short duration. We validate our method using synthetic data sets and demonstrate its applicability to real data sets from single molecule experiments on Holliday junctions labeled with conventional fluorescent dyes.
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Affiliation(s)
- Ioannis Sgouralis
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shreya Madaan
- School of Computing, Informatics, and Decision Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics, Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Rachael Kha
- School for Engineering of Matter, Transport and Energy , Arizona State University , Tempe , Arizona 85287 , United States
| | - Rizal F Hariadi
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States.,Biodesign Center for Molecular Design and Biomimetics, Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Steve Pressé
- Center for Biological Physics, Department of Physics , Arizona State University , Tempe , Arizona 85287 , United States.,School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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13
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Okamoto K, Sako Y. Single-Molecule Förster Resonance Energy Transfer Measurement Reveals the Dynamic Partially Ordered Structure of the Epidermal Growth Factor Receptor C-Tail Domain. J Phys Chem B 2019; 123:571-581. [PMID: 30571124 DOI: 10.1021/acs.jpcb.8b10066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) or regions (IDRs) are thought to exhibit unique functionalities without forming ordered structures. However, these molecular mechanisms are not easily elucidated, partly because of the difficultly of measuring structural information. In this study, we applied the alternative laser excitation (ALEX) method and circular dichroism (CD) spectroscopy to investigate the structure of the C-terminal tail (CTT) domain of the human epidermal growth factor receptor (EGFR). The single-molecule distributions of Förster resonance energy transfer (FRET) obtained by ALEX under solution conditions modified by the addition of potassium chloride (KCl), urea, or guanidinium chloride (GdmCl) allowed us to separately examine the influences of charge interactions and secondary structure formation. The CD spectrum analyses indicated the types of included secondary structure. The results suggested that the structure of the CTT is influenced by secondary structure formation, which is a principally antiparallel β-sheet, rather than by charge interactions and that phosphorylation of the major Grb2-binding sites partially denatures that secondary structure. Our findings suggest that the EGFR CTT might regulate ligand binding kinetics by local β-sheet formation or by the disruption associated with phosphorylation states.
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Affiliation(s)
- Kenji Okamoto
- Cellular Informatics Laboratory , RIKEN , 2-1 Hirosawa , Wako , Saitama 351-0198 Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory , RIKEN , 2-1 Hirosawa , Wako , Saitama 351-0198 Japan
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14
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Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems. Biophys Rev 2017; 10:317-326. [PMID: 29243093 PMCID: PMC5899725 DOI: 10.1007/s12551-017-0366-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/19/2017] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging (SMI) of proteins in operation has a history of intensive investigations over 20 years and is now widely used in various fields of biology and biotechnology. We review the recent advances in SMI of fluorescently-tagged proteins in structural biology, focusing on technical applicability of SMI to the measurements in living cells. Basic technologies and recent applications of SMI in structural biology are introduced. Distinct from other methods in structural biology, SMI directly observes single molecules and single-molecule events one-by-one, thus, explicitly analyzing the distribution of protein structures and the history of protein dynamics. It also allows one to detect single events of protein interaction. One unique feature of SMI is that it is applicable in complicated and heterogeneous environments, including living cells. The numbers, location, movements, interaction, oligomerization, and conformation of single-protein molecules have been determined using SMI in cellular systems.
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Okamoto K, Sako Y. Recent advances in FRET for the study of protein interactions and dynamics. Curr Opin Struct Biol 2017; 46:16-23. [PMID: 29800904 DOI: 10.1016/j.sbi.2017.03.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/20/2017] [Accepted: 03/20/2017] [Indexed: 11/20/2022]
Abstract
Förster/fluorescence resonance energy transfer (FRET) has been extensively used to detect the binding state or conformation of biomolecules. In the past few decades, various in vitro and in vivo applications of FRET measurement have been developed, including FRET probes, in-cell measurements, single-molecule measurements, and combination with computer simulation. In this review, we describe recent advances in FRET methods for examining biomolecular interactions and dynamics: (i) phasor plot analysis for quantitative analysis of protein interactions, (ii) single-molecule FRET measurement for detecting conformational dynamics in live cells, and (iii) data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein.
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Affiliation(s)
- Kenji Okamoto
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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