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Pleshakova TO, Ivanov YD, Valueva AA, Shumyantseva VV, Ilgisonis EV, Ponomarenko EA, Lisitsa AV, Chekhonin VP, Archakov AI. Analysis of Single Biomacromolecules and Viruses: Is It a Myth or Reality? Int J Mol Sci 2023; 24:1877. [PMID: 36768195 PMCID: PMC9915366 DOI: 10.3390/ijms24031877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
The beginning of the twenty-first century witnessed novel breakthrough research directions in the life sciences, such as genomics, transcriptomics, translatomics, proteomics, metabolomics, and bioinformatics. A newly developed single-molecule approach addresses the physical and chemical properties and the functional activity of single (individual) biomacromolecules and viral particles. Within the alternative approach, the combination of "single-molecule approaches" is opposed to "omics approaches". This new approach is fundamentally unique in terms of its research object (a single biomacromolecule). Most studies are currently performed using postgenomic technologies that allow the properties of several hundreds of millions or even billions of biomacromolecules to be analyzed. This paper discusses the relevance and theoretical, methodological, and practical issues related to the development potential of a single-molecule approach using methods based on molecular detectors.
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Trang VH, Rodgers ML, Boyle KJ, Hoskins AA, Strieter ER. Chemoenzymatic synthesis of bifunctional polyubiquitin substrates for monitoring ubiquitin chain remodeling. Chembiochem 2014; 15:1563-8. [PMID: 24961813 DOI: 10.1002/cbic.201402059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Indexed: 11/06/2022]
Abstract
Covalent attachment of ubiquitin to target proteins is one of the most pervasive post-translational modifications in eukaryotes. Target proteins are often modified with polymeric ubiquitin chains of defined lengths and linkages that may further undergo dynamic changes in composition in response to cellular signals. Biochemical characterization of the enzymes responsible for building and destroying ubiquitin chains is often thwarted by the lack of methods for preparation of the appropriate substrates containing probes for biochemical or biophysical studies. We have discovered that a yeast ubiquitin C-terminal hydrolase (Yuh1) also catalyzes transamidation reactions that can be exploited to prepare site-specifically modified polyubiquitin chains produced by thiol-ene chemistry. We have used this chemoenzymatic approach to prepare dual-functionalized ubiquitin chains containing fluorophore and biotin modifications. These dual-functionalized ubiquitin chains enabled the first real-time assay of ubiquitin chain disassembly by a human deubiquitinase (DUB) enzyme by single molecule fluorescence microscopy. In summary, this work provides a powerful new tool for elucidating the mechanisms of DUBs and other ubiquitin processing enzymes.
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Affiliation(s)
- Vivian H Trang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
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Claridge SA, Liao WS, Thomas JC, Zhao Y, Cao H, Cheunkar S, Serino AC, Andrews AM, Weiss PS. From the bottom up: dimensional control and characterization in molecular monolayers. Chem Soc Rev 2013; 42:2725-45. [PMID: 23258565 PMCID: PMC3596502 DOI: 10.1039/c2cs35365b] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale.
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Affiliation(s)
- Shelley A. Claridge
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Wei-Ssu Liao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John C. Thomas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yuxi Zhao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Huan Cao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Sarawut Cheunkar
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andrew C. Serino
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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Rospigliosi A, Ehlich R, Hoerber H, Middelberg A, Moggridge G. Electron transfer of plurimodified DNA SAMs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8264-71. [PMID: 17590024 DOI: 10.1021/la063704g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An STM-based current-voltage (I/V) investigation of deoxyribonucleic acid (DNA) 18 base pair (bp) oligonucleotide monolayers on gold is presented. Three bases of each of the immobilized and complementary strands were modified with either iodine or phenylethylene moieties. The oligonucleotides were immobilized on template stripped gold (tsg) surfaces and characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). AFM imaging showed that monolayers of the expected height were formed. A comparative study of normal, halogenated, and phenyl-modified DNA was made with the STM in tunneling spectroscopy (TS) mode. I/V spectroscopic measurements in the range +/-250 mV on both single- and double-stranded (ds) DNA monolayers (modified and unmodified) showed that for negative substrate bias (U(sub)) electron transfer is more efficient through a phenyl-modified monolayer than through normal or halogenated DNA. This effect was particularly clear below a threshold bias of -100 mV. For positive U(sub), unmodified ds DNA was found to conduct slightly better than the modified strands. This is presumably caused by greater order in the unmodified versus modified DNA monolayers. Modifications on the immobilized (thiolated) strand seem to improve electron transport through the DNA monolayer more than modifications on the complementary (not surface-bound) strand.
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Affiliation(s)
- Alessandro Rospigliosi
- Department of Chemical Engineering, University of Cambridge, Pembroke Street, New Museum Site, Cambridge, United Kingdom.
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Abstract
Biochemistry and structural biology are undergoing a dramatic revolution. Until now, we have tried to study subtle and complex biological processes by crude in vitro techniques, looking at average behaviors of vast numbers of molecules under conditions usually remote from those existing in the cell. Researchers have realized the limitations of this approach, but none other has been available. Now, we can not only observe the nuances of the behaviors of individual molecules but prod and probe them as well. Perhaps most important is the emerging ability to carry out such observations and manipulations within the living cell. The long-awaited leap to an in vivo biochemistry is at last underway.
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Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA.
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Tang J, Lin SH. Distance versus energy fluctuations and electron transfer in single protein molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:061108. [PMID: 16906810 DOI: 10.1103/physreve.73.061108] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Indexed: 05/11/2023]
Abstract
Stochastic nature due to distance and energy fluctuations of single protein molecules involved in electron-transfer (ET) reactions is studied. Distance fluctuations have been assumed previously for causing the slow fluctuations in the ET rates between a donor-acceptor pair constrained to a native protein. Although the observed t(-1/2) power law can be derived using Langevin dynamics with a simple chain model, some discrepancies exist. The friction coefficient and the Rouse segment time constant deduced from experimental data are several orders of magnitude too large, even though the extracted force constant is reasonable. Therefore, questions are raised about the distance-fluctuation mechanism and the activationless ET hypothesis. As an alternative mechanism, we considered fluctuations in activation energy and analyzed the data from two different single protein experiments to determine spectral distribution of energy fluctuations.
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Affiliation(s)
- Jau Tang
- Center for Ultrafast Science and Technology, California Institute of Technology, Pasadena, California 91125, USA.
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Weninger K, Bowen ME, Chu S, Brunger AT. Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations. Proc Natl Acad Sci U S A 2003; 100:14800-5. [PMID: 14657376 PMCID: PMC299806 DOI: 10.1073/pnas.2036428100] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vesicle fusion in eukaryotes is thought to involve the assembly of a highly conserved family of proteins termed soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) into a highly stable parallel four-helix bundle. We have used intermolecular single-molecule fluorescence resonance energy transfer to characterize preassembled neuronal SNARE complexes consisting of syntaxin, synaptobrevin, and synaptosome-associated protein of 25 kDa on deposited lipid bilayers. Surprisingly, we found a mixture of parallel as well as antiparallel configurations involving the SNARE motifs of syntaxin and synaptobrevin as well as those of syntaxin and synaptosome-associated protein of 25 kDa. The subpopulation with the parallel four-helix bundle configuration could be greatly enriched by an additional purification step in the presence of denaturant, indicating that the parallel configuration is the energetically most favorable state. Interconversion between the configurations was not observed. From this observation, we infer the conversion rate to be <1.5 h-1. The existence of antiparallel configurations suggests a regulatory role of chaperones, such as N-ethylmaleimide-sensitive factor, or the membrane environment during SNARE complex assembly in vivo, and it could be a partial explanation for the relatively slow rates of vesicle fusion observed by reconstituted fusion experiments in vitro.
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Affiliation(s)
- Keith Weninger
- The Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-4060, USA
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Andrec M, Levy RM, Talaga DS. Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. J Phys Chem A 2003; 107:7454-7464. [PMID: 19626138 PMCID: PMC2713777 DOI: 10.1021/jp035514+] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of fluorescence from single protein molecules has become an important new tool in the study of dynamic processes, allowing for the direct visualization of the motions experienced by individual proteins and macromolecular complexes. The data from such single-molecule experiments are in the form of photon trajectories, consisting of arrival times and wavelength information on individual photons. The analysis of photon trajectories can be difficult, particularly if the motions are occurring at rates comparable to the photon arrival rate or in the presence of noise. In this paper, we introduce the use of hidden Markov models (HMMs) for the analysis of photon trajectory data that operate using the photon data directly, without the need for ensemble averaging of the data as implied by correlation function analysis. Using a simple kinetic model, we examine the relationship between the uncertainty in the estimates of the motional rate and the photon detection rate. Remarkably, we obtain relative uncertainties in the rate constants of as little as 3% even when the interconversion rate is equal to the photon detection rate, and the uncertainty increases to only 10% when the interconversion rate is 10 times the photon detection rate. This suggests that useful information can be obtained for much faster kinetic regimes than have typically been studied. We also examine the impact of background photons on the determination of the rate and demonstrate that the HMM-based approach is robust, displaying small uncertainties for background photon arrival rates approaching that of the signal. These results not only are relevant in establishing the theoretical limits on precision, but are also useful in the context of experimental design. Finally, to demonstrate how the methodology can be extended to more complex kinetic models and how it can allow one to make use of the full power of statistics for purposes of model evaluation and selection, we consider a four-state kinetic model for protein conformational transitions previously studied by Schenter et al. (J. Phys. Chem. A1999, 103, 10477). We show how an HMM can be used as an alternative to higher-order correlation function analysis for the detection of "conformational memory" and apparent non-Markovian dynamics arising from such temporally inhomogeneous kinetic schemes.
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Affiliation(s)
- Michael Andrec
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854−8087
| | - Ronald M. Levy
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854−8087
| | - David S. Talaga
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854−8087
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Yasuda R, Masaike T, Adachi K, Noji H, Itoh H, Kinosita K. The ATP-waiting conformation of rotating F1-ATPase revealed by single-pair fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2003; 100:9314-8. [PMID: 12876203 PMCID: PMC170915 DOI: 10.1073/pnas.1637860100] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F1-ATPase is an ATP-driven rotary motor in which a rod-shaped gamma subunit rotates inside a cylinder made of alpha3beta3 subunits. To elucidate the conformations of rotating F1, we measured fluorescence resonance energy transfer (FRET) between a donor on one of the three betas and an acceptor on gamma in single F1 molecules. The yield of FRET changed stepwise at low ATP concentrations, reflecting the stepwise rotation of gamma. In the ATP-waiting state, the FRET yields indicated a gamma position approximately 40 degrees counterclockwise (= direction of rotation) from that in the crystal structures of mitochondrial F1, suggesting that the crystal structures mimic a metastable state before product release.
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Affiliation(s)
- Ryohei Yasuda
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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