1
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Jung W, Chen TY, Santiago AG, Chen P. Memory effects of transcription regulator-DNA interactions in bacteria. Proc Natl Acad Sci U S A 2024; 121:e2407647121. [PMID: 39361642 DOI: 10.1073/pnas.2407647121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/26/2024] [Indexed: 10/05/2024] Open
Abstract
Memory effect refers to the phenomenon where past events influence a system's current and future states or behaviors. In biology, memory effects often arise from intra- or intermolecular interactions, leading to temporally correlated behaviors. Single-molecule studies have shown that enzymes and DNA-binding proteins can exhibit time-correlated behaviors of their activity. While memory effects are well documented and studied in vitro, no such examples exist in cells to our knowledge. Combining single-molecule tracking (SMT) and single-cell protein quantitation, we find in living Escherichia coli cells distinct temporal correlations in the binding/unbinding events on DNA by MerR- and Fur-family metalloregulators, manifesting as memory effects with timescales of ~1 s. These memory effects persist irrespective of the type of the metalloregulators or their metallation states. Moreover, these temporal correlations of metalloregulator-DNA interactions are associated with spatial confinements of the metalloregulators near their DNA binding sites, suggesting microdomains of ~100 nm in size that possibly result from the spatial organizations of the bacterial chromosome without the involvement of membranes. These microdomains likely facilitate repeated binding events, enhancing regulator-DNA contact frequency and potentially gene regulation efficiency. These findings provide unique insights into the spatiotemporal dynamics of protein-DNA interactions in bacterial cells, introducing the concept of microdomains as a crucial player in memory effect-driven gene regulation.
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Affiliation(s)
- Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Tai-Yen Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Chemistry, University of Houston, Houston, TX 77204
| | - Ace George Santiago
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- 10x Genomics, Pleasanton, CA 94588
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
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2
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Hairil Anuar AH, Abd Ghafar SA, Hanafiah RM, Lim V, Mohd Pazli NFA. Critical Evaluation of Green Synthesized Silver Nanoparticles-Kaempferol for Antibacterial Activity Against Methicillin-Resistant Staphylococcus aureus. Int J Nanomedicine 2024; 19:1339-1350. [PMID: 38348172 PMCID: PMC10860521 DOI: 10.2147/ijn.s431499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/26/2023] [Indexed: 02/15/2024] Open
Abstract
Introduction This study aimed to characterize silver nanoparticles-kaempferol (AgNP-K) and its antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA). Green synthesis method was used to synthesize AgNP-K under the influence of temperature and different ratios of silver nitrate (AgNO3 and kaempferol). Methods AgNP-K 1:1 was synthesized with 1 mM kaempferol, whereas AgNP-K 1:2 with 2 mM kaempferol. The characterization of AgNP-K 1:1 and AgNP-K 1:2 was performed using UV-visible spectroscopy (UV-Vis), Zetasizer, transmission electron microscopy (TEM), scanning electron microscopy-dispersive X-ray spectrometer (SEM-EDX), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy. The antibacterial activities of five samples (AgNP-K 1:1, AgNP-K 1:2, commercial AgNPs, kaempferol, and vancomycin) at different concentrations (1.25, 2.5, 5, and 10 mg/mL) against MRSA were determined via disc diffusion assay (DDA), minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) assay, and time-kill assay. Results The presence of a dark brown colour in the solution indicated the formation of AgNP-K. The UV-visible absorption spectrum of the synthesized AgNP-K exhibited a broad peak at 447 nm. TEM, Zetasizer, and SEM-EDX results showed that the morphology and size of AgNP-K were nearly spherical in shape with 16.963 ± 6.0465 nm in size. XRD analysis confirmed that AgNP-K had a crystalline phase structure, while FTIR showed the absence of (-OH) group, indicating that kaempferol was successfully incorporated with silver. In DDA analysis, AgNP-K showed the largest inhibition zone (16.67 ± 1.19 mm) against MRSA as compared to kaempferol and commercial AgNPs. The MIC and MBC values for AgNP-K against MRSA were 1.25 and 2.50 mg/mL, respectively. The time-kill assay results showed that AgNP-K displayed bacteriostatic activity against MRSA. AgNP-K exhibited better antibacterial activity against MRSA when compared to commercial AgNPs or kaempferol alone.
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Affiliation(s)
- Ariff Haikal Hairil Anuar
- Department of Basic Sciences, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, 55100, Malaysia
| | - Siti Aisyah Abd Ghafar
- Department of Basic Sciences, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, 55100, Malaysia
| | - Rohazila Mohamad Hanafiah
- Department of Basic Sciences, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, 55100, Malaysia
| | - Vuanghao Lim
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang, 13200, Malaysia
| | - Nur Farah Atiqah Mohd Pazli
- Department of Basic Sciences, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, 55100, Malaysia
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3
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Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 PMCID: PMC7060211 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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4
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Wang Y, Horáček M, Zijlstra P. Strong Plasmon Enhancement of the Saturation Photon Count Rate of Single Molecules. J Phys Chem Lett 2020; 11:1962-1969. [PMID: 32073865 PMCID: PMC7061331 DOI: 10.1021/acs.jpclett.0c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Plasmon resonances have appeared as a promising method to boost the fluorescence intensity of single emitters. However, because research has focused on the enhancement at low excitation intensity, little is known about plasmon-fluorophore coupling near the point where the dye saturates. Here we study plasmon-enhanced fluorescence at a broad range of excitation intensities up to saturation. We adopt a novel DNA-mediated approach wherein dynamic single-molecule binding provides a controlled particle-fluorophore spacing, and dynamic rebinding circumvents artifacts due to photobleaching. We find that near saturation the maximum photon count rate is enhanced by more than 2 orders of magnitude at the optimal particle-fluorophore spacing, even for a dye with a high intrinsic quantum yield. We compare our results to a numerical model taking into account dye saturation. These experiments provide design rules to maximize the photon output of single emitters, which will open the door to studying fast dynamics in real time using single-molecule fluorescence.
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Affiliation(s)
- Yuyang Wang
- Department
of Applied Physics, Eindhoven University
of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
| | - Matěj Horáček
- Department
of Applied Physics, Eindhoven University
of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics, Eindhoven University
of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
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5
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Menges JA, Clasen A, Jourdain M, Beckmann J, Hoffmann C, König J, Jung G. Surface Preparation for Single-Molecule Chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2506-2516. [PMID: 30664351 DOI: 10.1021/acs.langmuir.8b03603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Immobilization procedures, intended to enable prolonged observation of single molecules by fluorescence microscopy, may generate heterogeneous microenvironments, thus inducing heterogeneity in the molecular behavior. On that account, we propose a straightforward surface preparation procedure for studying chemical reactions on the single-molecule level. Sensor fluorophores were developed, which exhibit dual-emissive characteristics in a homogeneously catalyzed showcase reaction. These molecules undergo a shift of fluorescence wavelength of about 100 nm upon Pd(0)-induced deallylation in the Tsuji-Trost reaction, allowing for separate visualization of the starting material and product. Whereas a simultaneous immobilization of dye and inert silane leads to strongly polydisperse reaction kinetics, a consecutive immobilization routine with deposition of dye molecules as the last step provides substrates underlying the kinetics of ensemble experiments. Also, the found kinetics are unaffected by the chemical variation of inert silanes, nearly uniform, and therefore well reproducible. Additional parameters like photostability, signal-to-noise ratio, dye-molecule density, and spatial distribution of dye molecules are, as well, hardly affected by surface modification in the successive immobilization scheme.
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Affiliation(s)
- Johannes A Menges
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Anne Clasen
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Matthias Jourdain
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julian Beckmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Caroline Hoffmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julien König
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Gregor Jung
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
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6
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Wu M, Lu HP. Oscillating Piconewton Force Manipulation on Single-Molecule Enzymatic Conformational and Reaction Dynamics. J Phys Chem B 2018; 122:12312-12321. [PMID: 30481025 DOI: 10.1021/acs.jpcb.8b08980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oscillation force has been demonstrated in theoretical studies as a critical role in unraveling the comprehensive enzymatic dynamics and addressing its regulation on enzyme activity. Utilizing the imposed external mechanical oscillation force by our newly developed magnetic tweezers coupled with a single-molecule photon-stamping imaging spectroscopic microscope, we experimentally studied a millisecond-scale oscillation force manipulation on single horseradish peroxidase enzymatic conformational and reaction dynamics. We have studied the enzymatic reaction dynamics and found that the enzyme activity changes under the real-time oscillatory force manipulation. Moreover, the oscillation force shows the capability of manipulating the enzyme active-site conformational state as well as the nascent-formed product's interaction with the active site of the enzyme, which impacts on the product release pathways. Specifically, we have identified that there are two product releasing pathways, the solvation-mediated diffusion releasing pathway and the spilling-out releasing pathway. We have observed that the spilling-out pathway can be significantly perturbed by the oscillatory force manipulation. Our correlated interpretation of enzymatic conformational and reaction dynamics provides a new insight into the comprehensive understanding of the complex conformational dynamics evolved in an enzymatic reaction. Technically, we have also demonstrated a novel approach capable of unfolding an enzyme under an enzymatic reaction condition in real time and, furthermore, by using an oscillatory mechanical weak piconewton force to manipulate enzyme conformations, and the enzyme thermal fluctuation is fully maintained. The real-time in situ fluorescence probe at the enzymatic active site reports the active-site conformational dynamics through each enzymatic reaction turnovers.
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Affiliation(s)
- Meiling Wu
- Department of Chemistry, Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - H Peter Lu
- Department of Chemistry, Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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7
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Xu Y, Gao Y, Su Y, Sun L, Xing F, Fan C, Li D. Single-Molecule Studies of Allosteric Inhibition of Individual Enzyme on a DNA Origami Reactor. J Phys Chem Lett 2018; 9:6786-6794. [PMID: 30412409 DOI: 10.1021/acs.jpclett.8b02992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Unraveling the conformational changes of enzymes together with inhibition kinetics during an enzymatic reaction has great potential in screening therapeutic candidates; however, it remains challenging due to the transient nature of each intermediate step. We report our study on the noncompetitive inhibition of horseradish peroxidase with single-turnover resolution using single-molecule fluorescence microscopy. By introducing DNA origami as an addressable nanoreactor, we observe the coexistence of nascent-formed fluorescent product on both catalytic and docking sites. We further propose a single-molecule kinetic model to reveal the interplay between product generation and noncompetitive inhibition and find three distinct inhibitor releasing pathways. Moreover, the kinetic isotope effect experiment indicates a strong correlation between catalytic and docking sites, suggesting an allosteric conformational change in noncompetitive inhibition. A memory effect is also observed. This work provides an in-depth understanding of the correlation between enzyme behavior and enzymatic conformational fluctuation, substrate conversion, and product releasing pathway and kinetics.
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Affiliation(s)
- Yan Xu
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- National Engineering Research Center for Nanotechnology , Shanghai 200241 , China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yingying Su
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Department of Chemistry, College of Science , Shanghai University , Shanghai 200444 , China
| | - Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Feifei Xing
- Department of Chemistry, College of Science , Shanghai University , Shanghai 200444 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Di Li
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
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8
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Kienle DF, Falatach RM, Kaar JL, Schwartz DK. Correlating Structural and Functional Heterogeneity of Immobilized Enzymes. ACS NANO 2018; 12:8091-8103. [PMID: 30067333 DOI: 10.1021/acsnano.8b02956] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.
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Affiliation(s)
- Daniel F Kienle
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Rebecca M Falatach
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
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9
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You S, Froberg J, Yu J, Haldar M, Sedigh A, Mallik S, Srivastava DK, Choi Y. Real-time monitoring of conformational transitions of single-molecule histone deacetylase 8 with nanocircuits. Chem Commun (Camb) 2018; 53:3307-3310. [PMID: 28261707 DOI: 10.1039/c6cc09949a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using single-molecule approaches, we directly observed the dynamic interaction between HDAC8 and various ligands as well as conformational interconversions during the catalytic reaction. Statistical analysis identified key kinetic parameters, demonstrating that the enzymatic activity is highly sensitive to both minor variations in the ligand structures and small synthetic molecules.
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Affiliation(s)
- Seungyong You
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
| | - James Froberg
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
| | - Junru Yu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Manas Haldar
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Abbas Sedigh
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, USA
| | - D K Srivastava
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
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10
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Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates. Curr Opin Chem Biol 2017; 41:43-49. [PMID: 29096323 DOI: 10.1016/j.cbpa.2017.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022]
Abstract
DNA polymerases must discriminate the correct Watson-Crick base pair-forming deoxynucleoside triphosphate (dNTP) substrate from three other dNTPs and additional triphosphates found in the cell. The rarity of misincorporations in vivo, then, belies the high tolerance for dNTP analogs observed in vitro. Advances over the last 10 years in single-molecule fluorescence and electronic detection of dNTP analog incorporation enable exploration of the mechanism and limits to base discrimination by DNA polymerases. Such studies reveal transient motions of DNA polymerase during substrate recognition and mutagenesis in the context of erroneous dNTP incorporation that can lead to evolution and genetic disease. Further improvements in time resolution and noise reduction of single-molecule studies will uncover deeper mechanistic understanding of this critical, first step in evolution.
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11
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Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation. Proc Natl Acad Sci U S A 2016; 113:15006-15011. [PMID: 27940917 DOI: 10.1073/pnas.1613404114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unraveling the conformational details of an enzyme during the essential steps of a catalytic reaction (i.e., enzyme-substrate interaction, enzyme-substrate active complex formation, nascent product formation, and product release) is challenging due to the transient nature of intermediate conformational states, conformational fluctuations, and the associated complex dynamics. Here we report our study on the conformational dynamics of horseradish peroxidase using single-molecule multiparameter photon time-stamping spectroscopy with mechanical force manipulation, a newly developed single-molecule fluorescence imaging magnetic tweezers nanoscopic approach. A nascent-formed fluorogenic product molecule serves as a probe, perfectly fitting in the enzymatic reaction active site for probing the enzymatic conformational dynamics. Interestingly, the product releasing dynamics shows the complex conformational behavior with multiple product releasing pathways. However, under magnetic force manipulation, the complex nature of the multiple product releasing pathways disappears and more simplistic conformations of the active site are populated.
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12
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XU Y, SUN LL, GAO YJ, QIN WW, PENG TH, LI D. Research Progresses in Single Molecule Enzymology. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Gül OT, Pugliese KM, Choi Y, Sims PC, Pan D, Rajapakse AJ, Weiss GA, Collins PG. Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths. BIOSENSORS-BASEL 2016; 6:bios6030029. [PMID: 27348011 PMCID: PMC5039648 DOI: 10.3390/bios6030029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 01/17/2023]
Abstract
As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.
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Affiliation(s)
- O Tolga Gül
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, Polatlı Faculty of Science and Arts, Gazi University, Polatlı 06900, Turkey
| | - Kaitlin M Pugliese
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA
| | - Yongki Choi
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Patrick C Sims
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Deng Pan
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Arith J Rajapakse
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697, USA.
| | - Philip G Collins
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA.
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14
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Schuabb V, Cinar S, Czeslik C. Effect of interfacial properties on the activation volume of adsorbed enzymes. Colloids Surf B Biointerfaces 2016; 140:497-504. [DOI: 10.1016/j.colsurfb.2016.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 01/24/2023]
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15
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Wang Z, Lu HP. Probing Single-Molecule Protein Spontaneous Folding–Unfolding Conformational Fluctuation Dynamics: The Multiple-State and Multiple-Pathway Energy Landscape. J Phys Chem B 2015; 119:6366-78. [DOI: 10.1021/acs.jpcb.5b00735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zijian Wang
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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16
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Świderek K, Tuñón I, Martí S, Moliner V. Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase. ACS Catal 2015; 5:1172-1185. [PMID: 25705562 DOI: 10.1021/cs501704f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last decade L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed from the 80s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction to take place. In this paper we show that the chemical step of the LDH catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single molecule spectrometry studies. Starting from a recently solved X-ray diffraction structure that presented an open loop conformation in two of the four chains of the tetramer, QM/MM free energy surfaces have been obtained at different levels of theory. Depending on the level of theory used to describe the electronic structure, the free energy barrier for the transformation of pyruvate into lactate with the open conformation of the protein varies between 12.9 and 16.3 kcal/mol, after quantizing the vibrations and adding the contributions of recrossing and tunneling effects. These values are very close to the experimentally deduced one (14.2 kcal·mol-1) and ~2 kcal·mol-1 smaller than the ones obtained with the closed loop conformer. Calculation of primary KIEs and IR spectra in both protein conformations are also consistent with our hypothesis and in agreement with experimental data. Our calculations suggest that the closure of the active site is mainly required for the inverse process; the oxidation of lactate to pyruvate. According to this hypothesis H4 type LDH enzyme molecules, where it has been propose that lactate is transformed into pyruvate, should have a better ability to close the mobile loop than the M4 type LDH molecules.
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Affiliation(s)
- Katarzyna Świderek
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Sergio Martí
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
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Schuabb V, Czeslik C. Activation volumes of enzymes adsorbed on silica particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15496-15503. [PMID: 25479476 DOI: 10.1021/la503605x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The immobilization of enzymes on carrier particles is useful in many biotechnological processes. In this way, enzymes can be separated from the reaction solution by filtering and can be reused in several cycles. On the other hand, there is a series of examples of free enzymes in solution that can be activated by the application of pressure. Thus, a potential loss of enzymatic activity upon immobilization on carrier particles might be compensated by pressure. In this study, we have determined the activation volumes of two enzymes, α-chymotrypsin (α-CT) and horseradish peroxidase (HRP), when they are adsorbed on silica particles and free in solution. The experiments have been carried out using fluorescence assays under pressures up to 2000 bar. In all cases, activation volumes were found to depend on the applied pressure, suggesting different compressions of the enzyme-substrate complex and the transition state. The volume profiles of free and adsorbed HRP are similar. For α-CT, larger activation volumes are found in the adsorbed state. However, up to about 500 bar, the enzymatic reaction of α-CT, which is adsorbed on silica particles, is characterized by a negative activation volume. This observation suggests that application of pressure might indeed be useful to enhance the activity of enzymes on carrier particles.
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Affiliation(s)
- Vitor Schuabb
- Department of Chemistry and Chemical Biology, TU Dortmund University , D-44221 Dortmund, Germany
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