1
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Jung W, Chen TY, Santiago AG, Chen P. Memory effects of transcription regulator-DNA interactions in bacteria. Proc Natl Acad Sci U S A 2024; 121:e2407647121. [PMID: 39361642 PMCID: PMC11474097 DOI: 10.1073/pnas.2407647121] [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: 04/20/2024] [Accepted: 08/26/2024] [Indexed: 10/05/2024] Open
Abstract
Memory effect refers to the phenomenon where past events influence a system's current and future states or behaviors. In biology, memory effects often arise from intra- or intermolecular interactions, leading to temporally correlated behaviors. Single-molecule studies have shown that enzymes and DNA-binding proteins can exhibit time-correlated behaviors of their activity. While memory effects are well documented and studied in vitro, no such examples exist in cells to our knowledge. Combining single-molecule tracking (SMT) and single-cell protein quantitation, we find in living Escherichia coli cells distinct temporal correlations in the binding/unbinding events on DNA by MerR- and Fur-family metalloregulators, manifesting as memory effects with timescales of ~1 s. These memory effects persist irrespective of the type of the metalloregulators or their metallation states. Moreover, these temporal correlations of metalloregulator-DNA interactions are associated with spatial confinements of the metalloregulators near their DNA binding sites, suggesting microdomains of ~100 nm in size that possibly result from the spatial organizations of the bacterial chromosome without the involvement of membranes. These microdomains likely facilitate repeated binding events, enhancing regulator-DNA contact frequency and potentially gene regulation efficiency. These findings provide unique insights into the spatiotemporal dynamics of protein-DNA interactions in bacterial cells, introducing the concept of microdomains as a crucial player in memory effect-driven gene regulation.
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Affiliation(s)
- Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Tai-Yen Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Department of Chemistry, University of Houston, Houston, TX77204
| | - Ace George Santiago
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- 10x Genomics, Pleasanton, CA94588
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
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2
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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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3
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. A Two-Armed Probe for In-Cell DEER Measurements on Proteins*. Chemistry 2020; 26:17128-17133. [PMID: 33200852 PMCID: PMC7839491 DOI: 10.1002/chem.202002743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Donny de Bruin
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Joeri A J Wondergem
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Doris Heinrich
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands.,Fraunhofer Institute for Silicate Research ISC, 97082, Würzburg, Germany
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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4
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Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 PMCID: PMC7060211 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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5
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Nandi S, Ghosh S, Bhattacharyya K. Live Cell Microscopy: A Physical Chemistry Approach. J Phys Chem B 2018; 122:3023-3036. [PMID: 29389140 DOI: 10.1021/acs.jpcb.7b11689] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing dynamics of intracellular components using physical chemistry techniques is a remarkable bottom-up approach for understanding the structures and functions of a biological cell. In this "Feature Article", we give an overview on local polarity, solvation, viscosity, acid-base property, red-ox processes (thiol-disulfide exchange), and gene silencing at selected intracellular components inside a live cell. Significant differences have been observed between cancer cells and their noncancer counterparts. We demonstrate that thiol-disulfide exchange, calcium oscillation, and gene silencing are manifested in time dependence of fluorescence intensity. We show that fluorescent gold nanoclusters may be used in drug delivery (e.g., doxorubicin) and selective killing of cancer cells. Further, we discuss dynamics and structural changes of DNA quadruplexes and i-motifs, induced by different external conditions (e.g., pH) and additives (e.g., K+ and other target specific small molecules). We demonstrate that peptidomimetic analogues have high specificity over double-stranded DNA for binding with i-motifs and G-quadruplexes. These results may have significant biological implications.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Jadavpur, Kolkata , 700 032 West Bengal , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-Indian Institute of Chemical Biology Campus , 4 Raja S. C. Mullick Road , Jadavpur, Kolkata 700 032 , India
| | - Kankan Bhattacharyya
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal , 462 066 Madhya Pradesh , India
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6
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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7
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Lu M, Lu HP. Revealing Multiple Pathways in T4 Lysozyme Substep Conformational Motions by Single-Molecule Enzymology and Modeling. J Phys Chem B 2017; 121:5017-5024. [DOI: 10.1021/acs.jpcb.7b03039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maolin Lu
- 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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8
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Amin MA, Nandi S, Mondal P, Mahata T, Ghosh S, Bhattacharyya K. Physical chemistry in a single live cell: confocal microscopy. Phys Chem Chem Phys 2017; 19:12620-12627. [DOI: 10.1039/c7cp02228j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A confocal microscope can be used to differentiate between cancer and non-cancer cells, and to enrich our knowledge of 3D tumor spheroids and drug delivery.
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Affiliation(s)
- Md. Asif Amin
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science (IACS)
- Jadavpur
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science (IACS)
- Jadavpur
- India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry Division
- Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Tanushree Mahata
- Organic and Medicinal Chemistry Division
- Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division
- Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Kankan Bhattacharyya
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhauri
- India
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9
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Chattoraj S, Bhattacharyya K. Biological oscillations: Fluorescence monitoring by confocal microscopy. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Guo Q, He Y, Lu HP. Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy. Proc Natl Acad Sci U S A 2015; 112:13904-9. [PMID: 26512103 PMCID: PMC4653173 DOI: 10.1073/pnas.1506405112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure-function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2-amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme-substrate interactions, enzyme-substrate active complex formation, and protein folding-binding interactions.
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Affiliation(s)
- Qing Guo
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Yufan He
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - H Peter Lu
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
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11
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Verma SD, Vanden Bout DA, Berg MA. When is a single molecule heterogeneous? A multidimensional answer and its application to dynamics near the glass transition. J Chem Phys 2015; 143:024110. [DOI: 10.1063/1.4926463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Sachin Dev Verma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - David A. Vanden Bout
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
| | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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12
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Lu B, Zhang B, Qi W, Zhu Y, Zhao Y, Zhou N, Sun R, Bao J, Wu C. Conformational study reveals amino acid residues essential for hemagglutinating and anti-proliferative activities of Clematis montana lectin. Acta Biochim Biophys Sin (Shanghai) 2014; 46:923-34. [PMID: 25239139 DOI: 10.1093/abbs/gmu085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clematis montana lectin (CML), a novel mannose-binding lectin purified from C. montana Buch.-Ham stem (Ranunculaceae), has been proved to have hemagglutinating activity in rabbit erythrocytes and apoptosis-inducing activity in tumor cells. However, the biochemical properties of CML have not revealed and its structural information still needs to be elucidated. In this study, it was found that CML possessed quite good thermostability and alkaline resistance, and its hemagglutinating activity was bivalent metal cation dependent. In addition, hemagglutination test and fluorescence spectroscopy proved that GuHCl, urea, and sodium dodecyl sulfate could change the conformation of CML and further caused the loss of hemagglutination activity. Moreover, the changes of fluorescence spectrum indicated that the tryptophan (Trp) microenvironment conversion might be related to the conformation and bioactivities of CML. In addition, it was also found that Trp residues, arginine (Arg) residues, and sulfhydryl were important for the hemagglutinating activity of CML, but only Trp was proved to be crucial for the CML conformation. Furthermore, the Trp, Arg, and sulfhydryl-modified CML exhibited 97.17%, 76.99%, and 49.64% loss of its anti-proliferative activity, respectively, which was consistent with the alterations of its hemagglutinating activity. Given these findings, Trp residues on the surface of CML are essential for the active center to form substrate-accessible conformation and suitable environment for carbohydrate binding.
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Affiliation(s)
- Bangmin Lu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Bin Zhang
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Wei Qi
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yanan Zhu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yan Zhao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Nan Zhou
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Rong Sun
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Jinku Bao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Chuanfang Wu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
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13
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Lu M, Lu HP. Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy. J Phys Chem B 2014; 118:11943-55. [PMID: 25222115 PMCID: PMC4199541 DOI: 10.1021/jp5081498] [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] [Indexed: 11/30/2022]
Abstract
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Conformational motions of proteins
are highly dynamic and intrinsically
complex. To capture the temporal and spatial complexity of conformational
motions and further to understand their roles in protein functions,
an attempt is made to probe multidimensional conformational dynamics
of proteins besides the typical one-dimensional FRET coordinate or
the projected conformational motions on the one-dimensional FRET coordinate.
T4 lysozyme hinge-bending motions between two domains along α-helix
have been probed by single-molecule FRET. Nevertheless, the domain
motions of T4 lysozyme are rather complex involving multiple coupled
nuclear coordinates and most likely contain motions besides hinge-bending.
It is highly likely that the multiple dimensional protein conformational
motions beyond the typical enzymatic hinged-bending motions have profound
impact on overall enzymatic functions. In this report, we have developed
a single-molecule multiparameter photon stamping spectroscopy integrating
fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic
approach enables simultaneous observations of both FRET-related site-to-site
conformational dynamics and molecular rotational (or orientational)
motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have
further observed wide-distributed rotational flexibility along orientation
coordinates by recording fluorescence anisotropy and simultaneously
identified multiple intermediate conformational states along FRET
coordinate by monitoring time-dependent donor lifetime, presenting
a whole picture of multidimensional conformational dynamics in the
process of T4 lysozyme open-close hinge-bending enzymatic turnover
motions under enzymatic reaction conditions. By analyzing the autocorrelation
functions of both lifetime and anisotropy trajectories, we have also
observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional
conformational fluctuation dynamics, providing a fundamental understanding
of the enzymatic reaction turnover dynamics associated with overall
enzyme as well as the specific active-site conformational fluctuations
that are not identifiable and resolvable in the conventional ensemble-averaged
experiment.
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Affiliation(s)
- Maolin Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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14
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Sasmal D, Lu HP. Single-molecule patch-clamp FRET microscopy studies of NMDA receptor ion channel dynamics in living cells: revealing the multiple conformational states associated with a channel at its electrical off state. J Am Chem Soc 2014; 136:12998-3005. [PMID: 25148304 PMCID: PMC4183623 DOI: 10.1021/ja506231j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Indexed: 01/10/2023]
Abstract
Conformational dynamics plays a critical role in the activation, deactivation, and open-close activities of ion channels in living cells. Such conformational dynamics is often inhomogeneous and extremely difficult to be directly characterized by ensemble-averaged spectroscopic imaging or only by single channel patch-clamp electric recording methods. We have developed a new and combined technical approach, single-molecule patch-clamp FRET microscopy, to probe ion channel conformational dynamics in living cell by simultaneous and correlated measurements of real-time single-molecule FRET spectroscopic imaging with single-channel electric current recording. Our approach is particularly capable of resolving ion channel conformational change rate process when the channel is at its electrically off states and before the ion channel is activated, the so-called "silent time" when the electric current signals are at zero or background. We have probed NMDA (N-methyl-D-aspartate) receptor ion channel in live HEK-293 cell, especially, the single ion channel open-close activity and its associated protein conformational changes simultaneously. Furthermore, we have revealed that the seemingly identical electrically off states are associated with multiple conformational states. On the basis of our experimental results, we have proposed a multistate clamshell model to interpret the NMDA receptor open-close dynamics.
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Affiliation(s)
- Dibyendu
Kumar Sasmal
- 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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15
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Zheng D, Lu HP. Single-molecule enzymatic conformational dynamics: spilling out the product molecules. J Phys Chem B 2014; 118:9128-40. [PMID: 25025461 PMCID: PMC4126733 DOI: 10.1021/jp5014434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 07/14/2014] [Indexed: 12/19/2022]
Abstract
Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses.
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Affiliation(s)
- Desheng Zheng
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
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16
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Ghosh S, Chattoraj S, Chowdhury R, Bhattacharyya K. Structure and dynamics of lysozyme in DMSO–water binary mixture: fluorescence correlation spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra00719k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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18
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Boghossian AA, Zhang J, Le Floch-Yin FT, Ulissi ZW, Bojo P, Han JH, Kim JH, Arkalgud JR, Reuel NF, Braatz RD, Strano MS. The chemical dynamics of nanosensors capable of single-molecule detection. J Chem Phys 2011; 135:084124. [DOI: 10.1063/1.3606496] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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