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Jaiswal S, He Y, Lu HP. Probing functional conformation-state fluctuation dynamics in recognition binding between calmodulin and target peptide. J Chem Phys 2022; 156:055102. [DOI: 10.1063/5.0074277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sunidhi Jaiswal
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Yufan He
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - H. Peter Lu
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, Ohio 43403, USA
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2
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Rico-Pasto M, Alemany A, Ritort F. Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways. J Phys Chem Lett 2022; 13:1025-1032. [PMID: 35072478 PMCID: PMC9882750 DOI: 10.1021/acs.jpclett.1c03521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply the Kramers kinetic diffusive model to derive the force-dependent kinetic rates of intermediate states from nonequilibrium pulling experiments. From the kinetic rates, we also extract the force-dependent kinetic barriers and the equilibrium folding energies. We apply our method to DNA hairpins with multiple folding pathways and intermediates. The experimental results agree with theoretical predictions. Furthermore, the proposed nonequilibrium single-molecule approach permits us to characterize kinetic and thermodynamic properties of native, unfolded, and intermediate states that cannot be derived from equilibrium hopping experiments.
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Affiliation(s)
- Marc Rico-Pasto
- Small
Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, C/Martí i Franqués 1, Barcelona, 08028, Spain
| | - Anna Alemany
- Department
of Anatomy and Embryology, Leiden University
Medical Center, Leiden, 2333ZC, The Netherlands
| | - Felix Ritort
- Small
Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, C/Martí i Franqués 1, Barcelona, 08028, Spain
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Kuang Y, Guo X, Guo A, Ran X, He Y, Zhang Y, Guo L. Single-molecule enzymatic reaction dynamics and mechanisms of GPX3 and TRXh9 from Arabidopsis thaliana. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 243:118778. [PMID: 32810779 DOI: 10.1016/j.saa.2020.118778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Glutathione peroxidases (GPXs) regulate the levels of reactive oxygen species in cells and tissues. During the redox cycling, the plant GPX is regenerated by thioredoxins (TRXs) as reductant rather than glutathione as the electron donor. However, the direct experimental observation on the interaction dynamics between GPXs and TRXs has not been reported, and the redox mechanism is unclear. In this work, the protein interactions between oxidized AtGPX3 and reduced AtTRXh9 have been studied using single-molecule fluorescence resonance energy transfer (smFRET). The obtained results indicate there are four processes in these two protein interaction, including biological recognition, binding, intermediate and unbinding state. Two enzymatic reaction intermediate states have been identified in the dissociation of AtGPX3-AtTRXh9 complex from binding to unbinding state, suggesting two types of interaction pathways and intermediate complexes. In particular, the dynamical study reveals that the redox reaction between oxidized AtGPX3 and reduced AtTRXh9 is realized through the forming and breaking of disulfide bonds via the active sites of Cys4 and Cys57 in AtTRXh9. These findings are of significant for deep understanding the redox reaction and mechanism between GPXs and TRXs enzymes, and studying other protein dynamics at single-molecule level.
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Affiliation(s)
- Yanmin Kuang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China; School of Physics and Electronics, International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, Henan University, Kaifeng 475004, China
| | - Xing Guo
- School of Physics and Electronics, International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, Henan University, Kaifeng 475004, China
| | - Aiyu Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China
| | - Xia Ran
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China; School of Physics and Electronics, International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, Henan University, Kaifeng 475004, China
| | - Yulu He
- School of Physics and Electronics, International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, Henan University, Kaifeng 475004, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China
| | - Lijun Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China; School of Physics and Electronics, International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, Henan University, Kaifeng 475004, China.
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4
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Gray TH, Yong EH. Effective diffusion in one-dimensional rough potential-energy landscapes. Phys Rev E 2020; 102:022138. [PMID: 32942433 DOI: 10.1103/physreve.102.022138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Diffusion in spatially rough, confining, one-dimensional continuous energy landscapes is treated using Zwanzig's proposal, which is based on the Smoluchowski equation. We show that Zwanzig's conjecture agrees with Brownian dynamics simulations only in the regime of small roughness. Our correction of Zwanzig's framework corroborates well with numerical results. A numerical simulation scheme based on our coarse-grained Langevin dynamics offers significant reductions in computational time. The mean first-passage time problem in the case of random roughness is treated. Finally, we address the validity of the separation of length scales assumption for the case of polynomial backgrounds and cosine-based roughness. Our results are applicable to hierarchical energy landscapes such as that of a protein's folding and transport processes in disordered media, where there is clear separation of length scale between smooth underlying potential and its rough perturbation.
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Affiliation(s)
- Thomas H Gray
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, Philippa Fawcett Drive, University of Cambridge, CB3 0AS, Cambridge, United Kingdom
- T.C.M. Group, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Ee Hou Yong
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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5
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Non-equilibrium protic and aprotic ionic liquids: Measuring the distance from the equilibrium state. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abe H, Takekiyo T, Yoshimura Y, Shimizu A, Ozawa S. Multiple crystal pathways and crystal polymorphs in protic ionic liquids. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Razgoniaeva N, Rogers S, Moroz P, Cassidy J, Zamkov M. Improving the spectral resolution in fluorescence microscopy through shaped-excitation imaging. Methods Appl Fluoresc 2018; 6:045006. [PMID: 30078787 DOI: 10.1088/2050-6120/aad81c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The visualization of distinct molecular species represents an important challenge of bio-imaging research. In past decades, the development of multicolor fluorescent (FL) labels has greatly improved our ability to track biological analytes, paving the way for important advances in understanding the cell dynamics. It remains challenging, however, to visualize a large number of different fluorephores simultaneously. Owing to a spectrally broad absorption of fluorescent dyes, only up to five color categories can be resolved at once. Here, we demonstrate a general strategy for distinguishing between multiple fluorescent targets in acquired microscopy images with improved accuracy. The present strategy is enabled through spectral shaping of the excitation light with an optical filter that uniquely attenuates the light absorption of each fluorophore in the investigated sample. The resulting emission changes, induced by such excitation modulation, are therefore target-specific and can be used for identifying various fluorescent species. The technique is demonstrated through an accurate identification of 8 different CdSe dyes with absorption maxima spanning the 520-620 spectral range. It is subsequently applied for accurate measurements of the pH balance in buffers emulating a metabolism of tumor cells.
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Affiliation(s)
- N Razgoniaeva
- The Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States of America. Department of Physics, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
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Wang Z, Lu HP. Single-Molecule Spectroscopy Study of Crowding-Induced Protein Spontaneous Denature and Crowding-Perturbed Unfolding–Folding Conformational Fluctuation Dynamics. J Phys Chem B 2018; 122:6724-6732. [DOI: 10.1021/acs.jpcb.8b03119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Zijiang Wang
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - H. Peter Lu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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Singh V, Biswas P. Estimating the mean first passage time of protein misfolding. Phys Chem Chem Phys 2018; 20:5692-5698. [PMID: 29410980 DOI: 10.1039/c7cp06918a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Most theoretical and experimental studies confirm that proteins fold in the time scale of microseconds to milliseconds, but the kinetics of the protein misfolding remains largely unexplored. The kinetics of unfolding-folding-misfolding equilibrium in proteins is formulated in the analytical framework of the Master equation. The folded, unfolded and the misfolded state are characterized in terms of their respective contacts. The Mean First Passage Time (MFPT) to acquire the misfolded conformation from the native or folded state is derived from this equation with different boundary conditions. The MFPT is found to be practically independent of the length of the protein, the number of native contacts and the rate constant for the misfolded to the folded state. The results obtained from the survival probability are directly correlated to the age of onset and appearance of misfolding diseases in humans.
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Affiliation(s)
- Vishal Singh
- Department of Chemistry, University of Delhi, Delhi-110007, India.
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Moroz P, Razgoniaeva N, He Y, Jensen G, Eckard H, Lu HP, Zamkov M. Tracking the Energy Flow on Nanoscale via Sample-Transmitted Excitation Photoluminescence Spectroscopy. ACS NANO 2017; 11:4191-4197. [PMID: 28324655 DOI: 10.1021/acsnano.7b01141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tracking the energy flow in nanoscale materials is an important yet challenging goal. Experimental methods for probing the intermolecular energy transfer (ET) are often burdened by the spectral crosstalk between donor and acceptor species, which complicates unraveling their individual contributions. This issue is particularly prominent in inorganic nanoparticles and biological macromolecules featuring broad absorbing profiles. Here, we demonstrate a general spectroscopic strategy for measuring the ET efficiency between nanostructured or molecular dyes exhibiting a significant donor-acceptor spectral overlap. The reported approach is enabled through spectral shaping of the broadband excitation light with solutions of donor molecules, which inhibits the excitation of respective donor species in the sample. The resulting changes in the acceptor emission induced by the spectral modulation of the excitation beam are then used to determine the quantum efficiency and the rate of ET processes between arbitrary fluorophores (molecules, nanoparticles, polymers) with high accuracy. The feasibility of the reported method was demonstrated using a control donor-acceptor system utilizing a protein-bridged Cy3-Cy5 dye pair and subsequently applied for studying the energy flow in a CdSe560-CdSe600 binary nanocrystal film.
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Affiliation(s)
- Pavel Moroz
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Natalia Razgoniaeva
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Yufan He
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Gregory Jensen
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Holly Eckard
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - H Peter Lu
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Mikhail Zamkov
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. NANOSCALE 2016; 8:19928-19944. [PMID: 27883140 PMCID: PMC5145784 DOI: 10.1039/c6nr06794h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.
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Affiliation(s)
- Dibyendu K Sasmal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura E Pulido
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Shan Kasal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Jun Huang
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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