1
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Wong CF, Leow CY, Grüber G. Cryo-EM structure of the Mycobacterium abscessus F 1-ATPase. Biochem Biophys Res Commun 2023; 671:140-145. [PMID: 37302287 DOI: 10.1016/j.bbrc.2023.05.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023]
Abstract
The cases of lung disease caused by non-tuberculous mycobacterium Mycobacterium abscessus (Mab) are increasing and not reliably curable. Repurposing of anti-tuberculosis inhibitors brought the oxidative phosphorylation pathway with its final product ATP, formed by the essential F1FO-ATP synthase (subunits α3:β3:γ:δ:ε:a:b:b':c9), into focus as an attractive inhibitor target against Mab. Because of the pharmacological attractiveness of this enzyme, we generated and purified a recombinant and enzymatically active Mab F1-ATPase complex, including subunits α3:β3:γ:δ:ε (MabF1-αβγδε) to achieve mechanistic, regulatory, and structural insights. The high purity of the complex enabled the first cryo-electron microscopy structure determination of the Mab F1-ATPase complex to 7.3 Å resolution. The enzyme showed low ATP hydrolysis activity, which was stimulated by trypsin treatment. No effect was observed in the presence of the detergent lauryldimethylamine oxide.
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Affiliation(s)
- Chui-Fann Wong
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Chen-Yen Leow
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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2
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Zhou Y, Lewis JH, Lu Z. Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules. eLife 2023; 12:82175. [PMID: 36800214 PMCID: PMC9937647 DOI: 10.7554/elife.82175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/15/2023] [Indexed: 02/18/2023] Open
Abstract
Most membrane protein molecules undergo conformational changes as they transition from one functional state to another one. An understanding of the mechanism underlying these changes requires the ability to resolve individual conformational states, whose changes often occur on millisecond and angstrom scales. Tracking such changes and acquiring a sufficiently large amount of data remain challenging. Here, we use the amino-acid transporter AdiC as an example to demonstrate the application of a high-resolution fluorescence-polarization-microscopy method in tracking multistate conformational changes of a membrane protein. We have successfully resolved four conformations of AdiC by monitoring the emission-polarization changes of a fluorophore label and quantified their probabilities in the presence of a series of concentrations of its substrate arginine. The acquired data are sufficient for determining all equilibrium constants that fully establish the energetic relations among the four states. The KD values determined for arginine in four individual conformations are statistically comparable to the previously reported overall KD determined using isothermal titration calorimetry. This demonstrated strong resolving power of the present polarization-microscopy method will enable an acquisition of the quantitative information required for understanding the expected complex conformational mechanism underlying the transporter's function, as well as those of other membrane proteins.
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Affiliation(s)
- Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - John H Lewis
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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3
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Volkán-Kacsó S, Marcus RA. F 1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory. Front Microbiol 2022; 13:861855. [PMID: 35531282 PMCID: PMC9072658 DOI: 10.3389/fmicb.2022.861855] [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: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
In this chapter, we review single-molecule observations of rotary motors, focusing on the general theme that their mechanical motion proceeds in substeps with each substep described by an angle-dependent rate constant. In the molecular machine F1-ATPase, the stepping rotation is described for individual steps by forward and back reaction rate constants, some of which depend strongly on the rotation angle. The rotation of a central shaft is typically monitored by an optical probe. We review our recent work on the theory for the angle-dependent rate constants built to treat a variety of single-molecule and ensemble experiments on the F1-ATPase, and relating the free energy of activation of a step to the standard free energy of reaction for that step. This theory, an elastic molecular transfer theory, provides a framework for a multistate model and includes the probe used in single-molecule imaging and magnetic manipulation experiments. Several examples of its application are the following: (a) treatment of the angle-dependent rate constants in stalling experiments, (b) use of the model to enhance the time resolution of the single-molecule imaging apparatus and to detect short-lived states with a microsecond lifetime, states hidden by the fluctuations of the imaging probe, (c) treatment of out-of-equilibrium "controlled rotation" experiments, (d) use of the model to predict, without adjustable parameters, the angle-dependent rate constants of nucleotide binding and release, using data from other experiments, and (e) insights obtained from correlation of kinetic and cryo-EM structural data. It is also noted that in the case where the release of ADP would be a bottleneck process, the binding of ATP to another site acts to accelerate the release by 5-6 orders of magnitude. The relation of the present set of studies to previous and current theoretical work in the field is described. An overall goal is to gain mechanistic insight into the biological function in relation to structure.
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Affiliation(s)
- Sándor Volkán-Kacsó
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
- Segerstrom Science Center, Azusa Pacific University, Azusa, CA, United States
| | - Rudolph A. Marcus
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
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4
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Sielaff H, Dienerowitz F, Dienerowitz M. Single-molecule FRET combined with electrokinetic trapping reveals real-time enzyme kinetics of individual F-ATP synthases. NANOSCALE 2022; 14:2327-2336. [PMID: 35084006 DOI: 10.1039/d1nr05754e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a key technique to observe conformational changes in molecular motors and to access the details of single-molecule static and dynamic disorder during catalytic processes. However, studying freely diffusing molecules in solution is limited to a few tens of milliseconds, while surface attachment often bears the risk to restrict their natural motion. In this paper we combine smFRET and electrokinetic trapping (ABEL trap) to non-invasively hold single FOF1-ATP synthases for up to 3 s within the detection volume, thereby extending the observation time by a factor of 10 as compared to Brownian diffusion without surface attachment. In addition, we are able to monitor complete reaction cycles and to selectively trap active molecules based on their smFRET signal, thus speeding up the data acquisition process. We demonstrate the capability of our method to study the dynamics of single molecules by recording the ATP-hydrolysis driven rotation of individual FOF1-ATP synthase molecules over numerous reaction cycles and extract their kinetic rates. We argue that our method is not limited to motor proteins. Instead, it can be applied to monitor conformational changes with millisecond time resolution for a wide range of enzymes, thereby making it a versatile tool for studying protein dynamics.
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Affiliation(s)
- Hendrik Sielaff
- Department of Chemistry, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2-4, 07743 Jena, Germany.
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5
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Abstract
Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic acid strands for DNA replication, recombination, and transcriptional regulation. Two evolutionarily distinct lineages of these enzymes, predicated on RecA and AAA+ ATPase folds, have been identified and characterized to date. Hexameric helicases couple NTP hydrolysis with conformational changes that move nucleic acid substrates through a central pore in the enzyme. How hexameric helicases productively engage client DNA or RNA segments and use successive rounds of NTPase activity to power translocation and unwinding have been longstanding questions in the field. Recent structural and biophysical findings are beginning to reveal commonalities in NTP hydrolysis and substrate translocation by diverse hexameric helicase families. Here, we review these molecular mechanisms and highlight aspects of their function that are yet to be understood.
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6
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Beckwith JS, Yang H. Information bounds in determining the 3D orientation of a single emitter or scatterer using point-detector-based division-of-amplitude polarimetry. J Chem Phys 2021; 155:144110. [PMID: 34654316 DOI: 10.1063/5.0065034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Determining the 3D orientation of a single molecule or particle, encoded in its polar and azimuthal angles, is of interest for a variety of fields, being relevant to a range of questions in elementary chemical reactivity, biomolecular motors, and nanorheology. A popular experimental method, known as division-of-amplitude polarimetry, for determining the real-time orientation of a single particle is to split the emitted/scattered light into multiple polarizations and to measure the light intensity using point detectors at these polarizations during a time interval Δt. Here, we derive the Cramér-Rao lower bounds for this method from the perspective of information theory in the cases of utilizing a chromophore or a scattering particle as a 3D orientation probe. Such Cramér-Rao lower bounds are new for using this experimental method to measure the full 3D orientation in both the scattering case and the fluorescence case. These results show that, for a scatterer, the information content of one photon is 1.16 deg-2 in the polar and 58.71 deg-2 in the azimuthal angles, respectively. For a chromophore, the information content of one photon is 2.54 deg-2 in the polar and 80.29 deg-2 in the azimuthal angles. In addition, the Cramér-Rao lower bound scales with the square root of the total signal photons. To determine orientation to an uncertainty of one degree requires 7.40 × 104 and 2.34 × 103 photons for the polar and the azimuthal angles, respectively, for fluorescence, whereas it takes 1.62 × 105 and 3.20 × 103 photons for scattering. This work provides experimentalists new guidelines by which future experiments can be designed and interpreted.
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Affiliation(s)
- Joseph S Beckwith
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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7
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The six steps of the complete F 1-ATPase rotary catalytic cycle. Nat Commun 2021; 12:4690. [PMID: 34344897 DOI: 10.1038/s41467-021-25029-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
F1Fo ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F1-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F1-ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F1-ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F1-ATPase catalytic cycle.
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8
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Measuring 3D orientation of nanocrystals via polarized luminescence of rare-earth dopants. Nat Commun 2021; 12:1943. [PMID: 33782386 PMCID: PMC8007814 DOI: 10.1038/s41467-021-22158-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/23/2021] [Indexed: 11/19/2022] Open
Abstract
Orientation of nanoscale objects can be measured by examining the polarized emission of optical probes. To retrieve a three-dimensional (3D) orientation, it has been essential to observe the probe (a dipole) along multiple viewing angles and scan with a rotating analyzer. However, this method requires a sophisticated optical setup and is subject to various external sources of error. Here, we present a fundamentally different approach employing coupled multiple emission dipoles that are inherent in lanthanide-doped phosphors. Simultaneous observation of different dipoles and comparison of their relative intensities allow to determine the 3D orientation from a single viewing angle. Moreover, the distinct natures of electric and magnetic dipoles originating in lanthanide luminescence enable an instant orientation analysis with a single-shot emission spectrum. We demonstrate a straightforward orientation analysis of Eu3+-doped NaYF4 nanocrystals using a conventional fluorescence microscope. Direct imaging of the rod-shaped nanocrystals proved the high accuracy of the measurement. This methodology would provide insights into the mechanical behaviors of various nano- and biomolecular systems. Determining the orientation of nanoscale objects in three-dimensional space has typically required complicated optical setups. Here, the authors develop a simple method to retrieve the 3D orientation of luminescent, lanthanide-doped nanorods from a single-shot emission spectrum.
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9
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Chen L, Wang M, Zhang X, Zhang M, Hu Y, Shi Z, Xi P, Gao J. Group-Sparsity-Based Super-Resolution Dipole Orientation Mapping. IEEE TRANSACTIONS ON MEDICAL IMAGING 2019; 38:2687-2694. [PMID: 30990177 DOI: 10.1109/tmi.2019.2910221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The dipole orientation of fluorophores could be resolved by fluorescence polarization microscopy (FPM), which in turn reveals structural specificity for the labeled organelles. Conventional FPM can detect only the averaged fluorescence anisotropy collected from dipoles within the diffraction-limited volume. Super-resolution dipole orientation mapping (SDOM) method, which applies sparse deconvolution and least square estimation to fluorescence polarization modulation data, achieves the dipole orientation measurement within a sub-diffraction focal area. However, during SDOM analysis, some pixels with fluorescence signal are not resolved with orientation for relatively small adjusted R2. Here we report group-sparsity-based SDOM (GS-SDOM), which utilizes the relevance of modulation sequences to effectively improve the SDOM reconstruction model. More credible resolved dipole orientations with higher adjusted R2 can be mapped and false positive estimation for local dipole orientation is vitally corrected. In addition to achieving the same spatial super-resolution as SDOM does, GS-SDOM accesses more morphological information with more credible orientations and more accurate local dipole distribution estimation. During the GS-SDOM analysis of actin filaments in mammalian kidney cells, the dipole orientation of fluorescence is detected always parallel to the direction of the actin filaments. Also with dipole orientation information extracted by GS-SDOM, the reconstructed visual circle from intensity dimension is discerned as jointed by double close filaments and 3-dimensional co-localization is accomplished in the intersection of actin filaments.
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10
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Zhanghao K, Chen X, Liu W, Li M, Liu Y, Wang Y, Luo S, Wang X, Shan C, Xie H, Gao J, Chen X, Jin D, Li X, Zhang Y, Dai Q, Xi P. Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy. Nat Commun 2019; 10:4694. [PMID: 31619676 PMCID: PMC6795901 DOI: 10.1038/s41467-019-12681-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/20/2019] [Indexed: 12/26/2022] Open
Abstract
Fluorescence polarization microscopy images both the intensity and orientation of fluorescent dipoles and plays a vital role in studying molecular structures and dynamics of bio-complexes. However, current techniques remain difficult to resolve the dipole assemblies on subcellular structures and their dynamics in living cells at super-resolution level. Here we report polarized structured illumination microscopy (pSIM), which achieves super-resolution imaging of dipoles by interpreting the dipoles in spatio-angular hyperspace. We demonstrate the application of pSIM on a series of biological filamentous systems, such as cytoskeleton networks and λ-DNA, and report the dynamics of short actin sliding across a myosin-coated surface. Further, pSIM reveals the side-by-side organization of the actin ring structures in the membrane-associated periodic skeleton of hippocampal neurons and images the dipole dynamics of green fluorescent protein-labeled microtubules in live U2OS cells. pSIM applies directly to a large variety of commercial and home-built SIM systems with various imaging modality. Polarization microscopy has been combined with single-molecule localization, but it’s often limited in either speed or resolution. Here the authors present polarized Structured Illumination Microscopy (pSIM), a method that uses polarized laser excitation to measure dye orientation during fast super-resolution live cell imaging.
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Affiliation(s)
- Karl Zhanghao
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
| | - Xingye Chen
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Wenhui Liu
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Meiqi Li
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China
| | - Yiqiong Liu
- PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
| | - Yiming Wang
- PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
| | - Sha Luo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Chunyan Shan
- College of Life Sciences, Peking University, 100871, Beijing, China
| | - Hao Xie
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Juntao Gao
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Xiaowei Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Xiangdong Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Zhang
- PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China.
| | - Peng Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
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11
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Lewis JH, Lu Z. Resolution of ångström-scale protein conformational changes by analyzing fluorescence anisotropy. Nat Struct Mol Biol 2019; 26:802-807. [PMID: 31488909 PMCID: PMC6822697 DOI: 10.1038/s41594-019-0274-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2019] [Indexed: 11/09/2022]
Abstract
Conformational changes within typical protein molecules are rapid and small, making their quantitative resolution challenging. These changes generally involve rotational motions and may thus be resolved by determining changes in the orientation of a fluorescent label that assumes a unique orientation in each conformation. Here, by analyzing fluorescence intensities collected using a polarization microscope at a rate of 50 frames per second, we follow the changes of 10-16° in the orientation of a single bifunctional rhodamine molecule attached to a regulator of conductance to K+ (RCK) domain of the MthK channel, and thus, the transitions between its three conformational states, with effective standard deviation (σ) of 2-5°. Based on available crystal structures, the position of the fluorophore's center differs by 3.4-8.1 Å among the states. Thus, the present approach allows the resolution of protein conformational changes involving ångström-scale displacements.
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Affiliation(s)
- John H Lewis
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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13
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Sumi T, Klumpp S. Is F 1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip. NANO LETTERS 2019; 19:3370-3378. [PMID: 31017791 DOI: 10.1021/acs.nanolett.9b01181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a chemomechanical network model of the rotary molecular motor F1-ATPase which quantitatively describes not only the rotary motor dynamics driven by ATP hydrolysis but also the ATP synthesis caused by forced reverse rotations. We observe a high reversibility of F1-ATPase, that is, the main cycle of ATP synthesis corresponds to the reversal of the main cycle in the hydrolysis-driven motor rotation. However, our quantitative analysis indicates that torque-induced mechanical slip without chemomechanical coupling occurs under high external torque and reduces the maximal efficiency of the free energy transduction to 40-80% below the optimal efficiency. Heat irreversibly dissipates not only through the viscous friction of the probe but also directly from the motor due to torque-induced mechanical slip. Such irreversible heat dissipation is a crucial limitation for achieving a 100% free-energy transduction efficiency with biological nanomachines because biomolecules are easily deformed by external torque.
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Affiliation(s)
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems , University of Göttingen , Friedrich-Hund-Platz 1 , 37077 Göttingen , Germany
- Department Theory and Bio-Systems , Max Planck Institute of Colloids and Interfaces , 14424 Potsdam , Germany
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14
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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15
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Murcia Rios A, Vahidi S, Dunn SD, Konermann L. Evidence for a Partially Stalled γ Rotor in F 1-ATPase from Hydrogen-Deuterium Exchange Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:14860-14869. [PMID: 30339028 DOI: 10.1021/jacs.8b08692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
F1-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α3β3. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F1-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F1 complexes operate with an intact rotor at any given time, but that the rotor tip is prone to occasional unfolding. A molecular dynamics (MD) strategy was developed to model the off-axis forces acting on γ. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns. Our data suggest that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get "stuck" (and unfold) sporadically while the remainder of γ continues to rotate. This scenario contrasts the traditional "greasy bearing" model that envisions smooth rotation of the γ C-terminal helix. The fragility of the apical rotor tip in F1-ATPase is attributed to the absence of a c10 ring that stabilizes the rotation axis in intact FoF1. Overall, the MD/HDX strategy introduced here appears well suited for interrogating the inner workings of molecular motors.
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Affiliation(s)
- Angela Murcia Rios
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Siavash Vahidi
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Stanley D Dunn
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
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16
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Benoit MPMH, Sosa H. Use of Single Molecule Fluorescence Polarization Microscopy to Study Protein Conformation and Dynamics of Kinesin-Microtubule Complexes. Methods Mol Biol 2018; 1665:199-216. [PMID: 28940071 DOI: 10.1007/978-1-4939-7271-5_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single molecule fluorescence polarization microscopy (smFPM) is a technique that enables to monitor changes in the orientation of a single labeled protein domain. Here we describe a smFPM microscope set-up and protocols to investigate conformational changes associated with the movement of motor proteins along cytoskeletal tracks.
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Affiliation(s)
- Matthieu P M H Benoit
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Hernando Sosa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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17
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Tutkus M, Marciulionis T, Sasnauskas G, Rutkauskas D. DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field. Biophys J 2017; 112:850-858. [PMID: 28297644 DOI: 10.1016/j.bpj.2017.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/06/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
The single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study interactions and conformational changes of biological molecules in the distance range from a few to 10 nm. In this study, we demonstrate a method to augment this range with longer distances. The method is based on the intensity changes of a tethered fluorophore, diffusing in the exponentially decaying evanescent excitation field. In combination with FRET it allowed us to reveal and characterize the dynamics of what had been inaccessible conformations of the DNA-protein complex. Our model system, restriction enzyme Ecl18kI, interacts with a FRET pair-labeled DNA fragment to form two different DNA loop conformations. The DNA-protein interaction geometry is such that the efficient FRET is expected for one of these conformations-"antiparallel" loop. In the alternative "parallel" loop, the expected distance between the dyes is outside the range accessible by FRET. Therefore, "antiparallel" looping is observed in a single-molecule time trajectory as discrete transitions to a state of high FRET efficiency. At the same time, transitions to a high-intensity state of the directly excited acceptor fluorophore on a DNA tether are due to a change of its average position in the evanescent field of excitation and can be associated with a loop of either "parallel" or "antiparallel" configuration. Simultaneous analysis of FRET and acceptor intensity trajectories then allows us to discriminate different DNA loop conformations and access the average lifetimes of different states.
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Affiliation(s)
- Marijonas Tutkus
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Tomas Marciulionis
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | | | - Danielis Rutkauskas
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania.
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18
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Ragunathan P, Sielaff H, Sundararaman L, Biuković G, Subramanian Manimekalai MS, Singh D, Kundu S, Wohland T, Frasch W, Dick T, Grüber G. The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation. J Biol Chem 2017; 292:11262-11279. [PMID: 28495884 PMCID: PMC5500794 DOI: 10.1074/jbc.m117.784959] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/11/2017] [Indexed: 01/30/2023] Open
Abstract
The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide 521PDEHVEALDEDKLAKEAVKV540 of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.
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Affiliation(s)
- Priya Ragunathan
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Hendrik Sielaff
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | | | - Dhirendra Singh
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Subhashri Kundu
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Thorsten Wohland
- the Departments of Biological Sciences and Chemistry and NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore, 14 Science Drive 4, Singapore 117557, Republic of Singapore, and
| | - Wayne Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Thomas Dick
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Gerhard Grüber
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore,
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19
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Ai G, Liu P, Ge H. Torque-coupled thermodynamic model for F_{o}F_{1}-ATPase. Phys Rev E 2017; 95:052413. [PMID: 28618520 DOI: 10.1103/physreve.95.052413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 01/23/2023]
Abstract
F_{o}F_{1}-ATPase is a motor protein complex that utilizes transmembrane ion flow to drive the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and phosphate (Pi). While many theoretical models have been proposed to account for its rotary activity, most of them focus on the F_{o} or F_{1} portions separately rather than the complex as a whole. Here, we propose a simple but new torque-coupled thermodynamic model of F_{o}F_{1}-ATPase. Solving this model at steady state, we find that the monotonic variation of each portion's efficiency becomes much more robust over a wide range of parameters when the F_{o} and F_{1} portions are coupled together, as compared to cases when they are considered separately. Furthermore, the coupled model predicts the dependence of each portion's kinetic behavior on the parameters of the other. Specifically, the power and efficiency of the F_{1} portion are quite sensitive to the proton gradient across the membrane, while those of the F_{o} portion as well as the related Michaelis constants for proton concentrations respond insensitively to concentration changes in the reactants of ATP synthesis. The physiological proton gradient across the membrane in the F_{o} portion is also shown to be optimal for the Michaelis constants of ADP and phosphate in the F_{1} portion during ATP synthesis. Together, our coupled model is able to predict key dynamic and thermodynamic features of the F_{o}F_{1}-ATPase in vivo semiquantitatively, and suggests that such coupling approach could be further applied to other biophysical systems.
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Affiliation(s)
- Guangkuo Ai
- Beijing International Center for Mathematical Research and School of Mathematical Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Pengfei Liu
- Applied and Computational Mathematics, California Institute of Technology, Pasadena, California 91125, USA
| | - Hao Ge
- Beijing International Center for Mathematical Research and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, People's Republic of China
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20
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Krajnik B, Chen J, Watson MA, Cockroft SL, Feringa BL, Hofkens J. Defocused Imaging of UV-Driven Surface-Bound Molecular Motors. J Am Chem Soc 2017; 139:7156-7159. [DOI: 10.1021/jacs.7b02758] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bartosz Krajnik
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - Jiawen Chen
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Matthew A. Watson
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Scott L. Cockroft
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Johan Hofkens
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
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21
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Fujimura S, Ito Y, Ikeguchi M, Adachi K, Yajima J, Nishizaka T. Dissection of the angle of single fluorophore attached to the nucleotide in corkscrewing microtubules. Biochem Biophys Res Commun 2017; 485:614-620. [PMID: 28257843 DOI: 10.1016/j.bbrc.2017.01.165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/28/2017] [Indexed: 11/18/2022]
Abstract
Direct dissection of the angles of single fluorophores under an optical microscope has been a challenging approach to study the dynamics of proteins in an aqueous solution. For angle quantifications of single substrates, however, there was only one report (Nishizaka et al., 2014) because of difficulties of construction of experimental systems with active proteins working at the single-molecule level. We here show precise estimation of orientation of single fluorescent nucleotides bound to single tubulins that comprise microtubule. When single-headed kinesins immobilized on a glass surface drive the sliding of microtubules, microtubules show corkscrewing with regular pitches (Yajima et al., 2005 & 2008). We found, by using a three-dimensional tracking microscope, that S8A mutant kinesin also showed precise corkscrewing with a 330-nm pitch, which is 13% longer than that of the wild type. The assay with the mutant was combined with a defocused imaging technique to visualize the rotational behavior of fluorescent nucleotide bound to corkscrewing microtubule. Notably, the defocused pattern of single TAMRA-GTP periodically changed, precisely correlating to its precession movement. The time course of the change in the fluorophore angle projected to the xy-plane enabled to estimate both the fluorophore orientation against microtubule axis and the precision of angle-determination of analyses system. The orientation showed main distribution with peaks at∼40°, 50° and 60°. To identify their molecular conformations, the rigorous docking simulations were performed using an atomic-level structure modeled by fitting x-ray crystal structures to the cryo-electron microscopy map. Among isomers, 2'-O-EDA-GDP labeled with 5- or 6-TAMRA were mainly specified as possible candidates as a substrate, which suggested the hydrolysis of TAMRA-GTP by tubulins.
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Affiliation(s)
- Shoko Fujimura
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Yuko Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Kengo Adachi
- Department of Physics, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts & Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
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22
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Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc 2016; 4:042004. [PMID: 28192292 PMCID: PMC5308470 DOI: 10.1088/2050-6120/4/4/042004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.
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23
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Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism. J Virol 2016; 90:8036-46. [PMID: 27356896 DOI: 10.1128/jvi.00508-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
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24
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Liu B, Böker A. Measuring rotational diffusion of colloidal spheres with confocal microscopy. SOFT MATTER 2016; 12:6033-6037. [PMID: 27353601 DOI: 10.1039/c6sm01082b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report an experimental method to measure the translational and rotational dynamics of colloidal spheres in three dimensions with confocal microscopy and show that the experimental values reasonably agree with the theoretical values. This method can be extended to study rotational dynamics in concentrated colloidal systems and complex bio-systems.
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Affiliation(s)
- Bing Liu
- Fraunhofer Institut für angewandte Polymerforschung (IAP), Geiselbergstr. 69, 14476 Potsdam, Germany. and DWI - Leibniz Institute for Interactive Materials e.V., Lehrstuhl für Makromolekulare Materialien und Oberflächen, RWTH Aachen University, Forckenbeckstr. 50, D-52056 Aachen, Germany and State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Alexander Böker
- Fraunhofer Institut für angewandte Polymerforschung (IAP), Geiselbergstr. 69, 14476 Potsdam, Germany. and DWI - Leibniz Institute for Interactive Materials e.V., Lehrstuhl für Makromolekulare Materialien und Oberflächen, RWTH Aachen University, Forckenbeckstr. 50, D-52056 Aachen, Germany and Lehrstuhl für Polymermaterialien und Polymertechnologien, Universität Potsdam, Geiselbergstrasse 69, 14476 Potsdam, Germany
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25
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Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional Studies of DNA-Protein Interactions Using FRET Techniques. Methods Mol Biol 2016; 1334:115-41. [PMID: 26404147 DOI: 10.1007/978-1-4939-2877-4_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of protein-DNA interactions.
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Affiliation(s)
- Simon Blouin
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Daniel A Lafontaine
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1.
| | - J Carlos Penedo
- School of Physics and Astronomy, University of St. Andrews, St. Andrews, UK
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26
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Abstract
Janus particles, named after the two-faced Roman god Janus, have different surface makeups, structures or compartments on two sides. This review highlights recent advances in employing Janus particles as novel analytical tools for live cell imaging and biosensing. Unlike conventional particles used in analytical science, two-faced Janus particles provide asymmetry and directionality, and can combine different or even incompatible properties within a single particle. The broken symmetry enables imaging and quantification of rotational dynamics, revealing information beyond what traditional measurements offer. The spatial segregation of molecules on the surface of a single particle also allows analytical functions that would otherwise interfere with each other to be decoupled, opening up opportunities for novel multimodal analytical methods. We summarize here the development of Janus particles, a few general methods for their fabrication and, more importantly, the emerging and novel applications of Janus particles as multi-functional imaging probes and sensors.
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Affiliation(s)
- Yi Yi
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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27
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Börner R, Ehrlich N, Hohlbein J, Hübner CG. Single Molecule 3D Orientation in Time and Space: A 6D Dynamic Study on Fluorescently Labeled Lipid Membranes. J Fluoresc 2016; 26:963-75. [DOI: 10.1007/s10895-016-1784-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
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28
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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29
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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30
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Pi F, Vieweger M, Zhao Z, Wang S, Guo P. Discovery of a new method for potent drug development using power function of stoichiometry of homomeric biocomplexes or biological nanomotors. Expert Opin Drug Deliv 2015; 13:23-36. [PMID: 26307193 DOI: 10.1517/17425247.2015.1082544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Multidrug resistance and the appearance of incurable diseases inspire the quest for potent therapeutics. AREAS COVERED We review a new methodology in designing potent drugs by targeting multi-subunit homomeric biological motors, machines or complexes with Z > 1 and K = 1, where Z is the stoichiometry of the target, and K is the number of drugged subunits required to block the function of the complex. The condition is similar to a series electrical circuit of Christmas decorations: failure of one light bulb causes the entire lighting system to lose power. In most multi-subunit, homomeric biological systems, a sequential coordination or cooperative action mechanism is utilized, thus K equals 1. Drug inhibition depends on the ratio of drugged to non-drugged complexes. When K = 1, and Z > 1, the inhibition effect follows a power law with respect to Z, leading to enhanced drug potency. The hypothesis that the potency of drug inhibition depends on the stoichiometry of the targeted biological complexes was recently quantified by Yang-Hui's Triangle (or binomial distribution), and proved using a highly sensitive in vitro phi29 viral DNA packaging system. Examples of targeting homomeric bio-complexes with high stoichiometry for potent drug discovery are discussed. EXPERT OPINION Biomotors with multiple subunits are widespread in viruses, bacteria and cells, making this approach generally applicable in the development of inhibition drugs with high efficiency.
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Affiliation(s)
- Fengmei Pi
- a 1 University of Kentucky, Nanobiotechnology Center , Lexington, KY 40536, USA.,b 2 University of Kentucky, Markey Cancer Center , Lexington, KY 40536, USA.,c 3 University of Kentucky, Department of Pharmaceutical Sciences , 789 S. Limestone Street, Room # 576, Lexington, KY 40536, USA +1 859 218 0128 ; +1 859 257 1307 ;
| | - Mario Vieweger
- a 1 University of Kentucky, Nanobiotechnology Center , Lexington, KY 40536, USA.,b 2 University of Kentucky, Markey Cancer Center , Lexington, KY 40536, USA.,c 3 University of Kentucky, Department of Pharmaceutical Sciences , 789 S. Limestone Street, Room # 576, Lexington, KY 40536, USA +1 859 218 0128 ; +1 859 257 1307 ;
| | - Zhengyi Zhao
- a 1 University of Kentucky, Nanobiotechnology Center , Lexington, KY 40536, USA.,b 2 University of Kentucky, Markey Cancer Center , Lexington, KY 40536, USA.,c 3 University of Kentucky, Department of Pharmaceutical Sciences , 789 S. Limestone Street, Room # 576, Lexington, KY 40536, USA +1 859 218 0128 ; +1 859 257 1307 ;
| | - Shaoying Wang
- a 1 University of Kentucky, Nanobiotechnology Center , Lexington, KY 40536, USA.,b 2 University of Kentucky, Markey Cancer Center , Lexington, KY 40536, USA.,c 3 University of Kentucky, Department of Pharmaceutical Sciences , 789 S. Limestone Street, Room # 576, Lexington, KY 40536, USA +1 859 218 0128 ; +1 859 257 1307 ;
| | - Peixuan Guo
- a 1 University of Kentucky, Nanobiotechnology Center , Lexington, KY 40536, USA.,b 2 University of Kentucky, Markey Cancer Center , Lexington, KY 40536, USA.,c 3 University of Kentucky, Department of Pharmaceutical Sciences , 789 S. Limestone Street, Room # 576, Lexington, KY 40536, USA +1 859 218 0128 ; +1 859 257 1307 ;
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31
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Wang L, Roth JS, Han X, Evans SD. Photosynthetic Proteins in Supported Lipid Bilayers: Towards a Biokleptic Approach for Energy Capture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3306-3318. [PMID: 25727786 DOI: 10.1002/smll.201403469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/11/2015] [Indexed: 06/04/2023]
Abstract
In nature, plants and some bacteria have evolved an ability to convert solar energy into chemical energy usable by the organism. This process involves several proteins and the creation of a chemical gradient across the cell membrane. To transfer this process to a laboratory environment, several conditions have to be met: i) proteins need to be reconstituted into a lipid membrane, ii) the proteins need to be correctly oriented and functional and, finally, iii) the lipid membrane should be capable of maintaining chemical and electrical gradients. Investigating the processes of photosynthesis and energy generation in vivo is a difficult task due to the complexity of the membrane and its associated proteins. Solid, supported lipid bilayers provide a good model system for the systematic investigation of the different components involved in the photosynthetic pathway. In this review, the progress made to date in the development of supported lipid bilayer systems suitable for the investigation of membrane proteins is described; in particular, there is a focus on those used for the reconstitution of proteins involved in light capture.
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Affiliation(s)
- Lei Wang
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
- State Key Laboratory of Urban Water Resource and Environment, School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Johannes S Roth
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Stephen D Evans
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
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32
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Fish J, Scrimgeour J. Fast weighted centroid algorithm for single particle localization near the information limit. APPLIED OPTICS 2015; 54:6360-6366. [PMID: 26193415 DOI: 10.1364/ao.54.006360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A simple weighting scheme that enhances the localization precision of center of mass calculations for radially symmetric intensity distributions is presented. The algorithm effectively removes the biasing that is common in such center of mass calculations. Localization precision compares favorably with other localization algorithms used in super-resolution microscopy and particle tracking, while significantly reducing the processing time and memory usage. We expect that the algorithm presented will be of significant utility when fast computationally lightweight particle localization or tracking is desired.
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Enoki S, Iino R, Niitani Y, Minagawa Y, Tomishige M, Noji H. High-speed angle-resolved imaging of a single gold nanorod with microsecond temporal resolution and one-degree angle precision. Anal Chem 2015; 87:2079-86. [PMID: 25647635 DOI: 10.1021/ac502408c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed two types of high-speed angle-resolved imaging methods for single gold nanorods (SAuNRs) using objective-type vertical illumination dark-field microscopy and a high-speed CMOS camera to achieve microsecond temporal and one-degree angle resolution. These methods are based on: (i) an intensity analysis of focused images of SAuNR split into two orthogonally polarized components and (ii) the analysis of defocused SAuNR images. We determined the angle precision (statistical error) and accuracy (systematic error) of the resultant SAuNR (80 nm × 40 nm) images projected onto a substrate surface (azimuthal angle) in both methods. Although both methods showed a similar precision of ∼1° for the azimuthal angle at a 10 μs temporal resolution, the defocused image analysis showed a superior angle accuracy of ∼5°. In addition, the polar angle was also determined from the defocused SAuNR images with a precision of ∼1°, by fitting with simulated images. By taking advantage of the defocused image method's full revolution measurement range in the azimuthal angle, the rotation of the rotary molecular motor, F1-ATPase, was measured with 3.3 μs temporal resolution. The time constants of the pauses waiting for the elementary steps of the ATP hydrolysis reaction and the torque generated in the mechanical steps have been successfully estimated. The high-speed angle-resolved SAuNR imaging methods will be applicable to the monitoring of the fast conformational changes of many biological molecular machines.
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Affiliation(s)
- Sawako Enoki
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo , Tokyo 113-8656, Japan
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34
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Nowak G, Bakajsova D. Protein kinase C-α interaction with F0F1-ATPase promotes F0F1-ATPase activity and reduces energy deficits in injured renal cells. J Biol Chem 2015; 290:7054-66. [PMID: 25627689 DOI: 10.1074/jbc.m114.588244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We showed previously that active PKC-α maintains F0F1-ATPase activity, whereas inactive PKC-α mutant (dnPKC-α) blocks recovery of F0F1-ATPase activity after injury in renal proximal tubules (RPTC). This study tested whether mitochondrial PKC-α interacts with and phosphorylates F0F1-ATPase. Wild-type PKC-α (wtPKC-α) and dnPKC-α were overexpressed in RPTC to increase their mitochondrial levels, and RPTC were exposed to oxidant or hypoxia. Mitochondrial levels of the γ-subunit, but not the α- and β-subunits, were decreased by injury, an event associated with 54% inhibition of F0F1-ATPase activity. Overexpressing wtPKC-α blocked decreases in γ-subunit levels, maintained F0F1-ATPase activity, and improved ATP levels after injury. Deletion of PKC-α decreased levels of α-, β-, and γ-subunits, decreased F0F1-ATPase activity, and hindered the recovery of ATP content after RPTC injury. Mitochondrial PKC-α co-immunoprecipitated with α-, β-, and γ-subunits of F0F1-ATPase. The association of PKC-α with these subunits decreased in injured RPTC overexpressing dnPKC-α. Immunocapture of F0F1-ATPase and immunoblotting with phospho(Ser) PKC substrate antibody identified phosphorylation of serine in the PKC consensus site on the α- or β- and γ-subunits. Overexpressing wtPKC-α increased phosphorylation and protein levels, whereas deletion of PKC-α decreased protein levels of α-, β-, and γ-subunits of F0F1-ATPase in RPTC. Phosphoproteomics revealed phosphorylation of Ser(146) on the γ subunit in response to wtPKC-α overexpression. We concluded that active PKC-α 1) prevents injury-induced decreases in levels of γ subunit of F0F1-ATPase, 2) interacts with α-, β-, and γ-subunits leading to increases in their phosphorylation, and 3) promotes the recovery of F0F1-ATPase activity and ATP content after injury in RPTC.
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Affiliation(s)
- Grażyna Nowak
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Diana Bakajsova
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
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35
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A unique mechanism of curcumin inhibition on F1 ATPase. Biochem Biophys Res Commun 2014; 452:940-4. [DOI: 10.1016/j.bbrc.2014.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/05/2014] [Indexed: 11/21/2022]
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36
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Knight AE. Single-molecule fluorescence imaging by total internal reflection fluorescence microscopy (IUPAC Technical Report). PURE APPL CHEM 2014. [DOI: 10.1515/pac-2012-0605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractTotal internal reflection fluorescence (TIRF) is a popular illumination technique in microscopy, with many applications in cell and molecular biology and biophysics. The chief advantage of the technique is the high contrast that can be achieved by restricting fluorescent excitation to a thin layer. We summarise the optical theory needed to understand the technique and various aspects required for a practical implementation of it, including the merits of different TIRF geometries. Finally, we discuss a variety of applications including super-resolution microscopy and high-throughput DNA sequencing technologies.
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Affiliation(s)
- Alex E. Knight
- 1Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
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37
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Ichimura T, Jin T, Fujita H, Higuchi H, Watanabe TM. Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles. Front Physiol 2014; 5:273. [PMID: 25120488 PMCID: PMC4114191 DOI: 10.3389/fphys.2014.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/05/2014] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies.
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Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan
| | - Takashi Jin
- Laboratory for Nano-Bio Probes, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideo Higuchi
- Department of Physics, School of Science, The University of Tokyo Bunkyo, Tokyo, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
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38
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Bockenhauer SD, Duncan TM, Moerner WE, Börsch M. The regulatory switch of F 1-ATPase studied by single-molecule FRET in the ABEL Trap. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8950:89500H. [PMID: 25309100 DOI: 10.1117/12.2042688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F1 (or FoF1) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F1. We investigate this proposed mechanism by labeling F1 specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F1 molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F1 in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F1 and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.
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Affiliation(s)
- Samuel D Bockenhauer
- Department of Chemistry, Stanford University, Stanford, CA, USA ; Department of Physics, Stanford University, Stanford, CA, USA
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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Duncan TM, Düser MG, Heitkamp T, McMillan DGG, Börsch M. Regulatory conformational changes of the ε subunit in single FRET-labeled F oF 1-ATP synthase. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8948:89481J. [PMID: 25076824 DOI: 10.1117/12.2040463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Subunit ε is an intrinsic regulator of the bacterial FoF1-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F1 portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme FoF1-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.
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Affiliation(s)
- Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Monika G Düser
- 3 Institute of Physics, Stuttgart University, Stuttgart, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Duncan G G McMillan
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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40
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An improved optical tweezers assay for measuring the force generation of single kinesin molecules. Methods Mol Biol 2014; 1136:171-246. [PMID: 24633799 DOI: 10.1007/978-1-4939-0329-0_10] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Numerous microtubule-associated molecular motors, including several kinesins and cytoplasmic dynein, produce opposing forces that regulate spindle and chromosome positioning during mitosis. The motility and force generation of these motors are therefore critical to normal cell division, and dysfunction of these processes may contribute to human disease. Optical tweezers provide a powerful method for studying the nanometer motility and piconewton force generation of single motor proteins in vitro. Using kinesin-1 as a prototype, we present a set of step-by-step, optimized protocols for expressing a kinesin construct (K560-GFP) in Escherichia coli, purifying it, and studying its force generation in an optical tweezers microscope. We also provide detailed instructions on proper alignment and calibration of an optical trapping microscope. These methods provide a foundation for a variety of similar experiments.
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41
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Kolomeisky AB. Motor proteins and molecular motors: how to operate machines at the nanoscale. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:463101. [PMID: 24100357 PMCID: PMC3858839 DOI: 10.1088/0953-8984/25/46/463101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Several classes of biological molecules that transform chemical energy into mechanical work are known as motor proteins or molecular motors. These nanometer-sized machines operate in noisy stochastic isothermal environments, strongly supporting fundamental cellular processes such as the transfer of genetic information, transport, organization and functioning. In the past two decades motor proteins have become a subject of intense research efforts, aimed at uncovering the fundamental principles and mechanisms of molecular motor dynamics. In this review, we critically discuss recent progress in experimental and theoretical studies on motor proteins. Our focus is on analyzing fundamental concepts and ideas that have been utilized to explain the non-equilibrium nature and mechanisms of molecular motors.
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Affiliation(s)
- Anatoly B. Kolomeisky
- Rice University, Department of Chemistry, 6100 Main Street, Houston, TX 77005-1892, USA
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42
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Nakanishi-Matsui M, Sekiya M, Futai M. Rotating proton pumping ATPases: subunit/subunit interactions and thermodynamics. IUBMB Life 2013; 65:247-54. [PMID: 23441040 DOI: 10.1002/iub.1134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 12/21/2012] [Indexed: 11/05/2022]
Abstract
In this article, we discuss single molecule observation of rotational catalysis by E. coli ATP synthase (F-ATPase) using small gold beads. Studies involving a low viscous drag probe showed the stochastic properties of the enzyme in alternating catalytically active and inhibited states. The importance of subunit interaction between the rotor and the stator, and thermodynamics of the catalysis are also discussed. "Single Molecule Enzymology" is a new trend for understanding enzyme mechanisms in biochemistry and physiology.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, and Futai Special Laboratory, Yahaba, Iwate, Japan.
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43
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Tanigawara M, Tabata KV, Ito Y, Ito J, Watanabe R, Ueno H, Ikeguchi M, Noji H. Role of the DELSEED loop in torque transmission of F1-ATPase. Biophys J 2013; 103:970-8. [PMID: 23009846 DOI: 10.1016/j.bpj.2012.06.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/23/2012] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
F(1)-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ-termed the DELSEED loop-is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F(1), suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F(1), whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α(3)β(3)-stator ring of the glycine mutant than in the wild-type F(1) and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions.
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Affiliation(s)
- Mizue Tanigawara
- Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
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44
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Watanabe R, Noji H. Chemomechanical coupling mechanism of F(1)-ATPase: catalysis and torque generation. FEBS Lett 2013; 587:1030-5. [PMID: 23395605 DOI: 10.1016/j.febslet.2013.01.063] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 11/18/2022]
Abstract
F1-ATPase (F1), a rotary motor protein driven by ATP hydrolysis, is unique with respect to its high efficiency and reversibility in converting chemical energy into mechanical work. Single-molecule studies have improved our understanding about the energy-conversion mechanism of F1 and the chemomechanical-coupling scheme under ATP hydrolysis conditions. A novel single-molecule technique was recently established to estimate the free-energy change of F1 during catalysis at elementary-step resolution, advancing our understanding about the energy-conversion mechanism of ATP hydrolysis and synthesis. The energy conversion mechanism of F1 elucidated from single-molecule studies provides us with important insights into the operating principles underlying molecular motors.
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Affiliation(s)
- Rikiya Watanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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45
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Adachi K, Oiwa K, Yoshida M, Nishizaka T, Kinosita K. Controlled rotation of the F₁-ATPase reveals differential and continuous binding changes for ATP synthesis. Nat Commun 2013; 3:1022. [PMID: 22929779 PMCID: PMC3449090 DOI: 10.1038/ncomms2026] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 07/27/2012] [Indexed: 11/23/2022] Open
Abstract
F1-ATPase is an ATP-driven rotary molecular motor that synthesizes ATP when rotated in reverse. To elucidate the mechanism of ATP synthesis, we imaged binding and release of fluorescently labelled ADP and ATP while rotating the motor in either direction by magnets. Here we report the binding and release rates for each of the three catalytic sites for 360° of the rotary angle. We show that the rates do not significantly depend on the rotary direction, indicating ATP synthesis by direct reversal of the hydrolysis-driven rotation. ADP and ATP are discriminated in angle-dependent binding, but not in release. Phosphate blocks ATP binding at angles where ADP binding is essential for ATP synthesis. In synthesis rotation, the affinity for ADP increases by >104, followed by a shift to high ATP affinity, and finally the affinity for ATP decreases by >104. All these angular changes are gradual, implicating tight coupling between the rotor angle and site affinities. Reverse rotation of the F1-ATPase results in the synthesis, rather than hydrolysis of ATP. Adachi et al. show that the molecular mechanism of ATP synthesis is the reverse of hydrolysis-driven rotation of the motor, and that ADP and ATP are discriminated by angle-dependent binding.
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Affiliation(s)
- Kengo Adachi
- Department of Physics, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan.
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46
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Börsch M. Microscopy of single F(o) F(1) -ATP synthases--the unraveling of motors, gears, and controls. IUBMB Life 2013; 65:227-37. [PMID: 23378185 DOI: 10.1002/iub.1149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/12/2013] [Indexed: 11/09/2022]
Abstract
Optical microscopy of single F(1) -ATPase and F(o) F(1) -ATP synthases started 15 years ago. Direct demonstration of ATP-driven subunit rotation by videomicroscopy became the new exciting tool to analyze the conformational changes of this enzyme during catalysis. Stimulated by these experiments, technical improvements for higher time resolution, better angular resolution, and reduced viscous drag were developed rapidly. Optics and single-molecule enzymology were entangled to benefit both biochemists and microscopists. Today, several single-molecule microscopy methods are established including controls for the precise nanomanipulation of individual enzymes in vitro. Förster resonance energy transfer, which has been used for simultaneous monitoring of conformational changes of different parts of this rotary motor, is one of them and may become the tool for the analysis of single F(o) F(1) -ATP synthases in membranes of living cells. Here, breakthrough experiments are critically reviewed and challenges are discussed for the future microscopy of single ATP synthesizing enzymes at work.
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Affiliation(s)
- Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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47
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Sielaff H, Börsch M. Twisting and subunit rotation in single F(O)(F1)-ATP synthase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120024. [PMID: 23267178 DOI: 10.1098/rstb.2012.0024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
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48
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Lesoine JF, Venkataraman PA, Maloney PC, Dumont M, Novotny L. Nanochannel-based single molecule recycling. NANO LETTERS 2012; 12:3273-8. [PMID: 22662745 PMCID: PMC3377747 DOI: 10.1021/nl301341m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering.
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Affiliation(s)
- John F. Lesoine
- Institute of Optics, University of Rochester, Rochester NY 14627
| | - Prahnesh A. Venkataraman
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Peter C. Maloney
- Department of Physiology, Johns Hopkins Medical School, Baltimore, MD, USA
| | - Mark Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Lukas Novotny
- Institute of Optics, University of Rochester, Rochester NY 14627
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49
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Sekiya M, Nakamoto RK, Nakanishi-Matsui M, Futai M. Binding of phytopolyphenol piceatannol disrupts β/γ subunit interactions and rate-limiting step of steady-state rotational catalysis in Escherichia coli F1-ATPase. J Biol Chem 2012; 287:22771-80. [PMID: 22582396 DOI: 10.1074/jbc.m112.374868] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In observations of single molecule behavior under V(max) conditions with minimal load, the F(1) sector of the ATP synthase (F-ATPase) rotates through continuous cycles of catalytic dwells (∼0.2 ms) and 120° rotation steps (∼0.6 ms). We previously established that the rate-limiting transition step occurs during the catalytic dwell at the initiation of the 120° rotation. Here, we use the phytopolyphenol, piceatannol, which binds to a pocket formed by contributions from α and β stator subunits and the carboxyl-terminal region of the rotor γ subunit. Piceatannol did not interfere with the movement through the 120° rotation step, but caused increased duration of the catalytic dwell. The duration time of the intrinsic inhibited state of F(1) also became significantly longer with piceatannol. All of the beads rotated at a lower rate in the presence of saturating piceatannol, indicating that the inhibitor stays bound throughout the rotational catalytic cycle. The Arrhenius plot of the temperature dependence of the reciprocal of the duration of the catalytic dwell (catalytic rate) indicated significantly increased activation energy of the rate-limiting step to trigger the 120° rotation. The activation energy was further increased by combination of piceatannol and substitution of γ subunit Met(23) with Lys, indicating that the inhibitor and the β/γ interface mutation affect the same transition step, even though they perturb physically separated rotor-stator interactions.
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Affiliation(s)
- Mizuki Sekiya
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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50
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Rotational catalysis in proton pumping ATPases: from E. coli F-ATPase to mammalian V-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1711-21. [PMID: 22459334 DOI: 10.1016/j.bbabio.2012.03.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 03/10/2012] [Accepted: 03/13/2012] [Indexed: 01/28/2023]
Abstract
We focus on the rotational catalysis of Escherichia coli F-ATPase (ATP synthase, F(O)F(1)). Using a probe with low viscous drag, we found stochastic fluctuation of the rotation rates, a flat energy pathway, and contribution of an inhibited state to the overall behavior of the enzyme. Mutational analyses revealed the importance of the interactions among β and γ subunits and the β subunit catalytic domain. We also discuss the V-ATPase, which has different physiological roles from the F-ATPase, but is structurally and mechanistically similar. We review the rotation, diversity of subunits, and the regulatory mechanism of reversible subunit dissociation/assembly of Saccharomyces cerevisiae and mammalian complexes. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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