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Hodge SR, Berg MA. Nonlinear measurements of kinetics and generalized dynamical modes. I. Extracting the one-dimensional Green's function from a time series. J Chem Phys 2021; 155:024122. [PMID: 34266246 DOI: 10.1063/5.0053422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Often, a single correlation function is used to measure the kinetics of a complex system. In contrast, a large set of k-vector modes and their correlation functions are commonly defined for motion in free space. This set can be transformed to the van Hove correlation function, which is the Green's function for molecular diffusion. Here, these ideas are generalized to other observables. A set of correlation functions of nonlinear functions of an observable is used to extract the corresponding Green's function. Although this paper focuses on nonlinear correlation functions of an equilibrium time series, the results are directly connected to other types of nonlinear kinetics, including perturbation-response experiments with strong fields. Generalized modes are defined as the orthogonal polynomials associated with the equilibrium distribution. A matrix of mode-correlation functions can be transformed to the complete, single-time-interval (1D) Green's function. Diagonalizing this matrix finds the eigendecays. To understand the advantages and limitation of this approach, Green's functions are calculated for a number of models of complex dynamics within a Gaussian probability distribution. Examples of non-diffusive motion, rate heterogeneity, and range heterogeneity are examined. General arguments are made that a full set of nonlinear 1D measurements is necessary to extract all the information available in a time series. However, when a process is neither dynamically Gaussian nor Markovian, they are not sufficient. In those cases, additional multidimensional measurements are needed.
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Affiliation(s)
- Stuart R Hodge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Mark A Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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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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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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Tavakoli M, Taylor JN, Li CB, Komatsuzaki T, Pressé S. Single Molecule Data Analysis: An Introduction. ADVANCES IN CHEMICAL PHYSICS 2017. [DOI: 10.1002/9781119324560.ch4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meysam Tavakoli
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - J. Nicholas Taylor
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
- Department of Mathematics; Stockholm University; 106 91 Stockholm Sweden
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Steve Pressé
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Cell and Integrative Physiology; Indiana University School of Medicine; Indianapolis IN 46202 USA
- Department of Physics and School of Molecular Sciences; Arizona State University; Tempe AZ 85287 USA
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Nagahata Y, Maeda S, Teramoto H, Horiyama T, Taketsugu T, Komatsuzaki T. Deciphering Time Scale Hierarchy in Reaction Networks. J Phys Chem B 2015; 120:1961-71. [DOI: 10.1021/acs.jpcb.5b09941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yutaka Nagahata
- Graduate
School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita 10,
Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Hiroshi Teramoto
- Graduate
School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0812, Japan
- Molecule
and Life Nonlinear Sciences Laboratory, Research Institute for Electronic
Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Takashi Horiyama
- Graduate
School of Science and Engineering, Saitama University, Shimo-Ookubo
255, Sakura-ku, Saitama 338-8570, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita 10,
Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Tamiki Komatsuzaki
- Graduate
School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0812, Japan
- Molecule
and Life Nonlinear Sciences Laboratory, Research Institute for Electronic
Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo 001-0020, Japan
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Taylor JN, Li CB, Cooper DR, Landes CF, Komatsuzaki T. Error-based extraction of states and energy landscapes from experimental single-molecule time-series. Sci Rep 2015; 5:9174. [PMID: 25779909 PMCID: PMC4361849 DOI: 10.1038/srep09174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/20/2015] [Indexed: 12/21/2022] Open
Abstract
Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.
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Affiliation(s)
- J Nicholas Taylor
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
| | - David R Cooper
- Department of Chemistry, Rice University, P.O. Box 1892, Houston. TX 77005
| | - Christy F Landes
- Department of Chemistry, Rice University, P.O. Box 1892, Houston. TX 77005
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
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Chen J, Poddar NK, Tauzin LJ, Cooper D, Kolomeisky AB, Landes CF. Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics. J Phys Chem B 2014; 118:12130-9. [PMID: 25254491 PMCID: PMC4207534 DOI: 10.1021/jp507067p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States
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