1
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Zhang S, Wang Z, Qiao J, Yu T, Zhang W. The effect of the loop on the thermodynamic and kinetic of single base pair in pseudoknot. J Chem Phys 2024; 161:085105. [PMID: 39212209 DOI: 10.1063/5.0216593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
RNA pseudoknots are RNA molecules with specialized three-dimensional structures that play important roles in various biological processes. To understand the functions and mechanisms of pseudoknots, it is essential to elucidate their structures and folding pathways. The most fundamental step in RNA folding is the opening and closing of a base pair. The effect of flexible loops on the base pair in pseudoknots remains unclear. In this work, we use molecular dynamics simulations and Markov state model to study the configurations, thermodynamic and kinetic of single base pair in pseudoknots. We find that the presence of the loop leads to a trap state. In addition, the rate-limiting step for the formation of base pair is the disruption of the trap state, rather than the open state to the closed state, which is quite different from the previous studies on non-pseudoknot RNA. For the thermodynamic parameters in pseudoknots, we find that the entropy difference upon opening the base pair between this simulation and the nearest-neighbor model results from the different entropy of different lengths of loop in solution. The thermodynamic parameters of the stack in pseudoknot are close to the nearest-neighbor parameters. The bases on the loop have different distribution patterns in different states, and the slow transition states of the loop are determined by the orientation of the bases.
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Affiliation(s)
- Shuhao Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Jie Qiao
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Ting Yu
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
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2
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Aguirre Rivera J, Mao G, Sabantsev A, Panfilov M, Hou Q, Lindell M, Chanez C, Ritort F, Jinek M, Deindl S. Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips. Science 2024; 385:892-898. [PMID: 39172826 DOI: 10.1126/science.adn5371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/12/2024] [Indexed: 08/24/2024]
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.
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Affiliation(s)
- J Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - G Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - A Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Q Hou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Lindell
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - C Chanez
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - M Jinek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - S Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
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3
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Gao C, Gao Q, Zhao C, Huo Y, Zhang Z, Yang J, Jia C, Guo X. Technologies for investigating single-molecule chemical reactions. Natl Sci Rev 2024; 11:nwae236. [PMID: 39224448 PMCID: PMC11367963 DOI: 10.1093/nsr/nwae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024] Open
Abstract
Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.
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Affiliation(s)
- Chunyan Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Qinghua Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Cong Zhao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Yani Huo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Zhizhuo Zhang
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Jinlong Yang
- Hefei National Research Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:866. [PMID: 37238735 PMCID: PMC10216711 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
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5
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Ojha AA, Srivastava A, Votapka LW, Amaro RE. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J Chem Inf Model 2023; 63:2469-2482. [PMID: 37023323 PMCID: PMC10131228 DOI: 10.1021/acs.jcim.2c01589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Janus kinases (JAK), a group of proteins in the nonreceptor tyrosine kinase (NRTKs) family, play a crucial role in growth, survival, and angiogenesis. They are activated by cytokines through the Janus kinase-signal transducer and activator of a transcription (JAK-STAT) signaling pathway. JAK-STAT signaling pathways have significant roles in the regulation of cell division, apoptosis, and immunity. Identification of the V617F mutation in the Janus homology 2 (JH2) domain of JAK2 leading to myeloproliferative disorders has stimulated great interest in the drug discovery community to develop JAK2-specific inhibitors. However, such inhibitors should be selective toward JAK2 over other JAKs and display an extended residence time. Recently, novel JAK2/STAT5 axis inhibitors (N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives) have displayed extended residence times (hours or longer) on target and adequate selectivity excluding JAK3. To facilitate a deeper understanding of the kinase-inhibitor interactions and advance the development of such inhibitors, we utilize a multiscale Markovian milestoning with Voronoi tessellations (MMVT) approach within the Simulation-Enabled Estimation of Kinetic Rates v.2 (SEEKR2) program to rank order these inhibitors based on their kinetic properties and further explain the selectivity of JAK2 inhibitors over JAK3. Our approach investigates the kinetic and thermodynamic properties of JAK-inhibitor complexes in a user-friendly, fast, efficient, and accurate manner compared to other brute force and hybrid-enhanced sampling approaches.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ambuj Srivastava
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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6
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Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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7
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Rodgers ML, Woodson SA. A roadmap for rRNA folding and assembly during transcription. Trends Biochem Sci 2021; 46:889-901. [PMID: 34176739 PMCID: PMC8526401 DOI: 10.1016/j.tibs.2021.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/14/2021] [Accepted: 05/27/2021] [Indexed: 01/11/2023]
Abstract
Ribonucleoprotein (RNP) assembly typically begins during transcription when folding of the newly synthesized RNA is coupled with the recruitment of RNA-binding proteins (RBPs). Upon binding, the proteins induce structural rearrangements in the RNA that are crucial for the next steps of assembly. Focusing primarily on bacterial ribosome assembly, we discuss recent work showing that early RNA-protein interactions are more dynamic than previously supposed, and remain so, until sufficient proteins are recruited to each transcript to consolidate an entire domain of the RNP. We also review studies showing that stable assembly of an RNP competes against modification and processing of the RNA. Finally, we discuss how transcription sets the timeline for competing and cooperative RNA-RBP interactions that determine the fate of the nascent RNA. How this dance is coordinated is the focus of this review.
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Affiliation(s)
- Margaret L Rodgers
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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8
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Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proc Natl Acad Sci U S A 2021; 118:2020837118. [PMID: 33658370 DOI: 10.1073/pnas.2020837118] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.
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9
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Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021; 12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) inherits the strategy of measurement from the effective "spectroscopic ruler" FRET and can be utilized to observe molecular behaviors with relatively high throughput at nanometer scale. The simplicity in principle and configuration of smFRET make it easy to apply and couple with other technologies to comprehensively understand single-molecule dynamics in various application scenarios. Despite its widespread application, smFRET is continuously developing and novel studies based on the advanced platforms have been done. Here, we summarize some representative examples of smFRET research of recent years to exhibit the versatility and note typical strategies to further improve the performance of smFRET measurement on different biomolecules.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yi Xing
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing 100191, China;
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
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10
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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11
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San Emeterio J, Pollack L. Visualizing a viral genome with contrast variation small angle X-ray scattering. J Biol Chem 2020; 295:15923-15932. [PMID: 32913117 PMCID: PMC7681021 DOI: 10.1074/jbc.ra120.013961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/04/2020] [Indexed: 01/14/2023] Open
Abstract
Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA.
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12
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Duss O, Stepanyuk GA, Puglisi JD, Williamson JR. Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding. Cell 2019; 179:1357-1369.e16. [PMID: 31761533 DOI: 10.1016/j.cell.2019.10.035] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
Ribosome assembly is an efficient but complex and heterogeneous process during which ribosomal proteins assemble on the nascent rRNA during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluorescence microscopy, we follow assembly of the entire 3' domain of the bacterial small ribosomal subunit in real time. We find that co-transcriptional rRNA folding is complicated by the formation of long-range RNA interactions and that r-proteins self-chaperone the rRNA folding process prior to stable incorporation into a ribonucleoprotein (RNP) complex. Assembly is initiated by transient rather than stable protein binding, and the protein-RNA binding dynamics gradually decrease during assembly. This work questions the paradigm of strictly sequential and cooperative ribosome assembly and suggests that transient binding of RNA binding proteins to cellular RNAs could provide a general mechanism to shape nascent RNA folding during RNP assembly.
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Affiliation(s)
- Olivier Duss
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Galina A Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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13
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Sansalone L, Zhang Y, Mazza MMA, Davis JL, Song KH, Captain B, Zhang HF, Raymo FM. High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores. J Phys Chem Lett 2019; 10:6807-6812. [PMID: 31622551 PMCID: PMC7427264 DOI: 10.1021/acs.jpclett.9b02250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A borondipyrromethene (BODIPY) chromophore is connected to a benzoxazole, benzothiazole, or nitrobenzothiazole heterocycle through an olefinic bridge with trans configuration. Rotation about the two [C-C] bonds flanking the olefinic bridge occurs with fast kinetics in solution, leading to the equilibration of four conformational isomers for each compound. Ensemble spectroscopic measurements in solutions fail to distinguish the coexisting isomers. They reveal instead averaged absorption and emission bands with dependence of the latter on the excitation wavelength. Using high-throughput single-molecule spectroscopy, two main populations of single molecules with distinct spectral centroids are observed for each compound on glass substrates. Computational analyses suggest the two populations of molecules to be conformational isomers with antiperiplanar and periplanar arrangements of the BODIPY chromophores about its [C-C] bond to the olefinic bridge. Thus, statistical analysis of multiple single-molecule emission spectra can discriminate stereoisomers that would otherwise be impossible to distinguish by ensemble measurements alone.
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Affiliation(s)
- Lorenzo Sansalone
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
- Corresponding Authors ,
| | - Mercedes M. A. Mazza
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Janel L. Davis
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Ki-Hee Song
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Burjor Captain
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Hao F. Zhang
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Françisco M. Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
- Corresponding Authors ,
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14
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Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophys J 2019; 117:1674-1683. [PMID: 31590890 DOI: 10.1016/j.bpj.2019.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kinetic Monte Carlo simulation, we investigate the kinetics mechanism of RNA helix-terminal basepairing. The study reveals a six-state folding scheme with three dominant folding pathways of tens, hundreds, and thousands of nanoseconds of folding timescales, respectively. The overall kinetics is rate limited by the detrapping of a misfolded state with the overall folding time of 10-5 s. Moreover, the analysis examines the different roles of the various driving forces, such as the basepairing and stacking interactions and the ion binding/dissociation effects on structural changes. The results may provide useful insights for developing a basepair opening/closing rate model and further kinetics models of large RNAs.
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15
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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16
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Samanta S, Gong W, Li W, Sharma A, Shim I, Zhang W, Das P, Pan W, Liu L, Yang Z, Qu J, Kim JS. Organic fluorescent probes for stochastic optical reconstruction microscopy (STORM): Recent highlights and future possibilities. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Duss O, Stepanyuk GA, Grot A, O'Leary SE, Puglisi JD, Williamson JR. Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts. Nat Commun 2018; 9:5087. [PMID: 30504830 PMCID: PMC6269517 DOI: 10.1038/s41467-018-07423-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation. The early steps of ribosome assembly occur co-transcriptionally on the nascent ribosomal RNA. Here the authors demonstrate an approach that allows simultaneous monitoring of transcription and ribosomal protein assembly at the single-molecule level in real time.
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Affiliation(s)
- Olivier Duss
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA
| | - Galina A Stepanyuk
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Annette Grot
- Department of Research and Development, Pacific Biosciences Inc, Menlo Park, CA, 94025, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA.,Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA.
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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18
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Gibbs DR, Kaur A, Megalathan A, Sapkota K, Dhakal S. Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope. Methods Protoc 2018; 1:mps1040040. [PMID: 31164580 PMCID: PMC6481079 DOI: 10.3390/mps1040040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023] Open
Abstract
Prism-based total internal reflection fluorescence (pTIRF) microscopy is one of the most widely used techniques for the single molecule analysis of a vast range of samples including biomolecules, nanostructures, and cells, to name a few. It allows for excitation of surface bound molecules/particles/quantum dots via evanescent field of a confined region of space, which is beneficial not only for single molecule detection but also for analysis of single molecule dynamics and for acquiring kinetics data. However, there is neither a commercial microscope available for purchase nor a detailed guide dedicated for building this microscope. Thus far, pTIRF microscopes are custom-built with the use of a commercially available inverted microscope, which requires high level of expertise in selecting and handling sophisticated instrument-parts. To directly address this technology gap, here we describe a step-by-step guide on how to build and characterize a pTIRF microscope for in vitro single-molecule imaging, nanostructure analysis and other life sciences research.
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Affiliation(s)
- Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
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19
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Maity BK, Vishvakarma V, Surendran D, Rawat A, Das A, Pramanik S, Arfin N, Maiti S. Spontaneous Fluctuations Can Guide Drug Design Strategies for Structurally Disordered Proteins. Biochemistry 2018; 57:4206-4213. [PMID: 29928798 DOI: 10.1021/acs.biochem.8b00504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structure-based "rational" drug design strategies fail for diseases associated with intrinsically disordered proteins (IDPs). However, structural disorder allows large-amplitude spontaneous intramolecular dynamics in a protein. We demonstrate a method that exploits this dynamics to provide quantitative information about the degree of interaction of an IDP with other molecules. A candidate ligand molecule may not bind strongly, but even momentary interactions can be expected to perturb the fluctuations. We measure the amplitude and frequency of the equilibrium fluctuations of fluorescently labeled small oligomers of hIAPP (an IDP associated with type II diabetes) in a physiological solution, using nanosecond fluorescence cross-correlation spectroscopy. We show that the interterminal distance fluctuates at a characteristic time scale of 134 ± 10 ns, and 6.4 ± 0.2% of the population is in the "closed" (quenched) state at equilibrium. These fluctuations are affected in a dose-dependent manner by a series of small molecules known to reduce the toxicity of various amyloid peptides. The degree of interaction increases in the following order: resveratrol < epicatechin ∼ quercetin < Congo red < epigallocatechin 3-gallate. Such ordering can provide a direction for exploring the chemical space for finding stronger-binding ligands. We test the biological relevance of these measurements by measuring the effect of these molecules on the affinity of hIAPP for lipid vesicles and cell membranes. We find that the ability of a molecule to modulate intramolecular fluctuations correlates well with its ability to lower membrane affinity. We conclude that structural disorder may provide new avenues for rational drug design for IDPs.
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Affiliation(s)
- Barun Kumar Maity
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Vicky Vishvakarma
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Dayana Surendran
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Anoop Rawat
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Anirban Das
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Shreya Pramanik
- UM-DAE Centre for Excellence in Basic Sciences , University of Mumbai , Kalina, Mumbai 400098 , India
| | - Najmul Arfin
- Center for Interdisciplinary Research in Basic Sciences , Jamia Milia Islamia , New Delhi 110025 , India
| | - Sudipta Maiti
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road , Colaba, Mumbai 400005 , India
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20
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SUN LL, SU YY, GAO YJ, Li W, LYU H, LI B, LI D. Progresses of Single Molecular Fluorescence Resonance Energy Transfer in Studying Biomacromolecule Dynamic Process. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61088-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Wiercigroch E, Staniszewska-Slezak E, Szkaradek K, Wojcik T, Ozaki Y, Baranska M, Malek K. FT-IR Spectroscopic Imaging of Endothelial Cells Response to Tumor Necrosis Factor-α: To Follow Markers of Inflammation Using Standard and High-Magnification Resolution. Anal Chem 2018; 90:3727-3736. [PMID: 29504750 DOI: 10.1021/acs.analchem.7b03089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two endothelial cell lines were selected as models to investigate an effect of incubation with cytokine tumor necrosis factor type α (TNF-α) using Fourier transform infrared (FT-IR) imaging spectroscopy. Both cell lines are often used in laboratories and are typical lung vascular endothelial cells (HMLVEC) derived from the fusion of umbilical vein endothelial cells with lung adenocarcinoma cells (EA.hy926). This study was focused on alteration of spectral changes accompanying inflammation at the cellular level by applying two resolution systems of FT-IR microscopy. The standard approach, with a pixel size of ca. 5.5 μm2, determined the inflammatory state of the whole cell, while a high-magnification resolution (pixel size of ca. 1.1 μm2) provided information at the subcellular level. Importantly, the analysis of IR spectra recorded with different modes produced similar results overall and yielded unambiguous classification of inflamed cells. Generally, the most significant changes in the cells under the influence of TNF-α are related with lipids-their composition and concentration; however, segregation of cells into subcellular compartments provided an additional insight into proteins and nucleic acids related events. The observed spectral alterations are specific for the type of endothelial cell line.
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Affiliation(s)
- Ewelina Wiercigroch
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | | | - Kinga Szkaradek
- Jagiellonian Centre for Experimental Therapeutics , Jagiellonian University , Bobrzynskiego 14 , 30-348 Krakow , Poland
| | - Tomasz Wojcik
- Jagiellonian Centre for Experimental Therapeutics , Jagiellonian University , Bobrzynskiego 14 , 30-348 Krakow , Poland
| | - Yukihiro Ozaki
- Department of Chemistry , School of Science and Technology, Kwansei Gakuin University , Gakuen 2-1 , Sanda , Hyogo 669-1337 , Japan
| | - Malgorzata Baranska
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland.,Jagiellonian Centre for Experimental Therapeutics , Jagiellonian University , Bobrzynskiego 14 , 30-348 Krakow , Poland
| | - Kamilla Malek
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
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23
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Cai H, Depoil D, Muller J, Sheetz MP, Dustin ML, Wind SJ. Spatial Control of Biological Ligands on Surfaces Applied to T Cell Activation. Methods Mol Biol 2018; 1584:307-331. [PMID: 28255709 DOI: 10.1007/978-1-4939-6881-7_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this chapter, we present techniques, based on molecular-scale nanofabrication and selective self-assembly, for the presentation of biomolecules of interest (ligands, receptors, etc.) on a surface with precise spatial control and arbitrary geometry at the single-molecule level. Metallic nanodot arrays are created on glass coverslips and are then used as anchors for the immobilization of biological ligands via thiol linking chemistry. The nanodot size is controlled by both lithography and metallization. The reagent concentration in self-assembly can be adjusted to ensure single-molecule occupancy for a given dot size. The surrounding glass is backfilled by a protein-repellent layer to prevent nonspecific adsorption. Moreover, bifunctional surfaces are created, whereby a second ligand is presented on the background, which is frequently a requirement for simulating complex cellular functions involving more than one key ligand. This platform serves as a novel and powerful tool for molecular and cellular biology, e.g., to study the fundamental mechanisms of receptor-mediated signaling.
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Affiliation(s)
- Haogang Cai
- Department of Mechanical Engineering, Columbia University, New York, USA
| | - David Depoil
- Kennedy Institute of Rheumatology, NDORMS, The University of Oxford, Oxford, UK
| | - James Muller
- Department of Pathology, Skirball Institute, New York University School of Medicine, New York, USA
| | - Michael P Sheetz
- Department of Biological Sciences, Columbia University, New York, USA.,National University of Singapore, Singapore, Singapore
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, NDORMS, The University of Oxford, Oxford, UK.,Department of Pathology, Skirball Institute, New York University School of Medicine, New York, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, 500 W 120th St, New York, NY, 10027, USA.
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24
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 350] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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25
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Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems. Biophys Rev 2017; 10:317-326. [PMID: 29243093 PMCID: PMC5899725 DOI: 10.1007/s12551-017-0366-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/19/2017] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging (SMI) of proteins in operation has a history of intensive investigations over 20 years and is now widely used in various fields of biology and biotechnology. We review the recent advances in SMI of fluorescently-tagged proteins in structural biology, focusing on technical applicability of SMI to the measurements in living cells. Basic technologies and recent applications of SMI in structural biology are introduced. Distinct from other methods in structural biology, SMI directly observes single molecules and single-molecule events one-by-one, thus, explicitly analyzing the distribution of protein structures and the history of protein dynamics. It also allows one to detect single events of protein interaction. One unique feature of SMI is that it is applicable in complicated and heterogeneous environments, including living cells. The numbers, location, movements, interaction, oligomerization, and conformation of single-protein molecules have been determined using SMI in cellular systems.
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26
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Flores MC, Márquez EA, Mora JR. Molecular modeling studies of bromopyrrole alkaloids as potential antimalarial compounds: a DFT approach. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2107-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Abeysirigunawardena SC, Kim H, Lai J, Ragunathan K, Rappé MC, Luthey-Schulten Z, Ha T, Woodson SA. Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes. Nat Commun 2017; 8:492. [PMID: 28887451 PMCID: PMC5591316 DOI: 10.1038/s41467-017-00536-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/05/2017] [Indexed: 01/09/2023] Open
Abstract
Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5′ domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure. Ribosomes assemble through the hierarchical addition of proteins to a ribosomal RNA scaffold. Here the authors use three-color single-molecule FRET to show how the dynamics of the rRNA dictate the order in which multiple proteins assemble on the 5′ domain of the E. coli 16S rRNA.
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Affiliation(s)
- Sanjaya C Abeysirigunawardena
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.,Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Jonathan Lai
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600S. Mathews Avenue, Urbana, IL, 61801, USA
| | - Kaushik Ragunathan
- Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48103, USA
| | - Mollie C Rappé
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.,Sandia National Laboratory, Sandia,, 87185-1468, NM, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600S. Mathews Avenue, Urbana, IL, 61801, USA
| | - Taekjip Ha
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA. .,Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Biophysics and Biophysical Chemistry and Department of Biomedical Engineering, Johns Hopkins University, Baltimore,, 21205, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, 21205, USA.
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.
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28
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Jazi AA, Ploetz E, Arizki M, Dhandayuthapani B, Waclawska I, Krämer R, Ziegler C, Cordes T. Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments. Biochemistry 2017; 56:2031-2041. [PMID: 28362086 PMCID: PMC5390306 DOI: 10.1021/acs.biochem.6b00916] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Caged
organic fluorophores are established tools for localization-based
super-resolution imaging. Their use relies on reversible deactivation
of standard organic fluorophores by chemical reduction or commercially
available caged dyes with ON switching of the fluorescent signal by
ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores
and caged rhodamine dyes, i.e., chemical deactivation of fluorescence,
for single-molecule Förster resonance energy transfer (smFRET)
experiments with freely diffusing molecules. They allow temporal separation
and sorting of multiple intramolecular donor–acceptor pairs
during solution-based smFRET. We use this “caged FRET”
methodology for the study of complex biochemical species such as multisubunit
proteins or nucleic acids containing more than two fluorescent labels.
Proof-of-principle experiments and a characterization of the uncaging
process in the confocal volume are presented. These reveal that chemical
caging and UV reactivation allow temporal uncoupling of convoluted
fluorescence signals from, e.g., multiple spectrally similar donor
or acceptor molecules on nucleic acids. We also use caging without
UV reactivation to remove unwanted overlabeled species in experiments
with the homotrimeric membrane transporter BetP. We finally outline
further possible applications of the caged FRET methodology, such
as the study of weak biochemical interactions, which are otherwise
impossible with diffusion-based smFRET techniques because of the required
low concentrations of fluorescently labeled biomolecules.
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Affiliation(s)
- Atieh Aminian Jazi
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Muhamad Arizki
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | - Izabela Waclawska
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Reinhard Krämer
- Institute for Biochemistry, Universität Köln , 50674 Köln, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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Kinz-Thompson CD, Bailey NA, Gonzalez RL. Precisely and Accurately Inferring Single-Molecule Rate Constants. Methods Enzymol 2016; 581:187-225. [PMID: 27793280 PMCID: PMC5746875 DOI: 10.1016/bs.mie.2016.08.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state vs time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal vs time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restricts the precision of these approaches and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories.
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Affiliation(s)
| | - N A Bailey
- Columbia University, New York, NY, United States
| | - R L Gonzalez
- Columbia University, New York, NY, United States.
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31
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Cai H, Wind SJ. Improved Glass Surface Passivation for Single-Molecule Nanoarrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10034-10041. [PMID: 27622455 PMCID: PMC5050166 DOI: 10.1021/acs.langmuir.6b02444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single-molecule fluorescence techniques provide a critical tool for probing biomolecular and cellular interactions with unprecedented resolution and precision. Unfortunately, many of these techniques are hindered by a common problem, namely, the nonspecific adsorption of target biomolecules. This issue is mostly addressed by passivating the glass surfaces with a poly(ethylene glycol) (PEG) brush. This is effective only at low concentrations of the probe molecule because there are defects inherent to polymer brushes formed on glass coverslips due to the presence of surface impurities. Tween-20, a detergent, is a promising alternative that can improve surface passivation, but it is incompatible with living cells, and it also possesses limited selectivity for glass background over metallic nanoparticles, which are frequently used as anchors for the probe molecules. To address these issues, we have developed a more versatile method to improve the PEG passivation. A thin film of hydrogen silsesquioxane (HSQ) is spin-coated and thermally cured on glass coverslips in order to cover the surface impurities. This minimizes the formation of PEG defects and reduces nonspecific adsorption, resulting in an improvement comparable to Tween-20 treatment. This approach was applied to single-molecule nanoarrays of streptavidin bound to AuPd nanodots patterned by e-beam lithography (EBL). The fluorescence signal to background ratio (SBR) on HSQ-coated glass was improved by ∼4-fold as compared to PEG directly on glass. This improvement enables direct imaging of ordered arrays of single molecules anchored to lithographically patterned arrays of metallic nanodots.
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Affiliation(s)
- Haogang Cai
- Dept. of Mechanical Engineering, Columbia University, New York 10027, USA
| | - Shalom J. Wind
- Dept. of Applied Physics and Applied Mathematics, Columbia University, New York 10027, USA
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32
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Lawrence MG, Shamsuzzaman M, Kondopaka M, Pascual C, Zengel JM, Lindahl L. The extended loops of ribosomal proteins uL4 and uL22 of Escherichia coli contribute to ribosome assembly and protein translation. Nucleic Acids Res 2016; 44:5798-810. [PMID: 27257065 PMCID: PMC4937340 DOI: 10.1093/nar/gkw493] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 05/21/2016] [Indexed: 11/13/2022] Open
Abstract
Nearly half of ribosomal proteins are composed of a domain on the ribosome surface and a loop or extension that penetrates into the organelle's RNA core. Our previous work showed that ribosomes lacking the loops of ribosomal proteins uL4 or uL22 are still capable of entering polysomes. However, in those experiments we could not address the formation of mutant ribosomes, because we used strains that also expressed wild-type uL4 and uL22. Here, we have focused on ribosome assembly and function in strains in which loop deletion mutant genes are the only sources of uL4 or uL22 protein. The uL4 and uL22 loop deletions have different effects, but both mutations result in accumulation of immature particles that do not accumulate in detectable amounts in wild-type strains. Thus, our results suggest that deleting the loops creates kinetic barriers in the normal assembly pathway, possibly resulting in assembly via alternate pathway(s). Furthermore, deletion of the uL4 loop results in cold-sensitive ribosome assembly and function. Finally, ribosomes carrying either of the loop-deleted proteins responded normally to the secM translation pausing peptide, but the uL4 mutant responded very inefficiently to the cmlAcrb pause peptide.
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Affiliation(s)
- Marlon G Lawrence
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Maithri Kondopaka
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Clarence Pascual
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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33
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Banterle N, Lemke EA. Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol 2016; 39:105-112. [PMID: 26990172 PMCID: PMC7611743 DOI: 10.1016/j.copbio.2016.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) can offer favorably high signal-to-noise observation of biological mechanisms. TIRFM can be used routinely to observe even single fluorescent molecules for a long duration (several seconds) at millisecond time resolution. However, to keep the investigated sample in the evanescent field, chemical surface immobilization techniques typically need to be implemented. In this review, we describe some of the recently developed novel nanodevices that overcome this limitation enabling long-term observation of free single molecules and outline their biological applications. The working concept of many devices is compatible with high-throughput strategies, which will further help to establish unbiased single molecule observation as a routine tool in biology to study the molecular underpinnings of even the most complex biological mechanisms.
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Affiliation(s)
- Niccolò Banterle
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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34
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Lavergne T, Lamichhane R, Malyshev DA, Li Z, Li L, Sperling E, Williamson JR, Millar DP, Romesberg FE. FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs. ACS Chem Biol 2016; 11:1347-53. [PMID: 26942998 DOI: 10.1021/acschembio.5b00952] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosome assembly has been studied intensively using Förster resonance energy transfer (FRET) with fluorophore-labeled fragments of RNA produced by chemical synthesis. However, these studies are limited by the size of the accessible RNA fragments. We have developed a replicable unnatural base pair (UBP) formed between (d)5SICS and (d)MMO2 or (d)NaM, which efficiently directs the transcription of RNA containing unnatural nucleotides. We now report the synthesis and evaluation of several of the corresponding ribotriphosphates bearing linkers that enable the chemoselective attachment of different functionalities. We found that the RNA polymerase from T7 bacteriophage does not incorporate NaM derivatives but does efficiently incorporate 5SICS(CO), whose linker enables functional group conjugation via Click chemistry, and when combined with the previously identified MMO2(A), whose amine side chains permits conjugation via NHS coupling chemistry, enables site-specific double labeling of transcribed RNA. To study ribosome assembly, we transcribed RNA corresponding to a 243-nt fragment of the central domain of Thermus thermophilus 16S rRNA containing 5SICS(CO) and MMO2(A) at defined locations and then site-specifically attached the fluorophores Cy3 and Cy5. FRET was characterized using single-molecule total internal reflection fluorescence (smTIRF) microscopy in the presence of various combinations of added ribosomal proteins. We demonstrate that each of the fragment's two three-helix junctions exist in open and closed states, with the latter favored by sequential protein binding. These results elucidate early and previously uncharacterized folding events underlying ribosome assembly and demonstrate the applicability of UBPs for biochemical, structural, and functional studies of RNAs.
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Affiliation(s)
- Thomas Lavergne
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Rajan Lamichhane
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Denis A. Malyshev
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Zhengtao Li
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Lingjun Li
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Edit Sperling
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - James R. Williamson
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - David P. Millar
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department
of Chemistry and ‡Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
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35
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Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR. Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly. J Mol Biol 2016; 428:3615-31. [PMID: 27192112 DOI: 10.1016/j.jmb.2016.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/02/2016] [Accepted: 05/07/2016] [Indexed: 11/18/2022]
Abstract
Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652-654 and 752-754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652-654 and 752-754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg(2+)- and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function.
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MESH Headings
- DNA Mutational Analysis
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Fluorescence Resonance Energy Transfer
- Genetic Complementation Test
- Macromolecular Substances/metabolism
- Magnesium/metabolism
- Models, Biological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Interaction Maps
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Kris Ann Baker
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Rajan Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Tek Lamichhane
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA; Section of Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Single Molecule Imaging Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK.
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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36
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Shi X, Huang L, Lilley DMJ, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 2016; 12:146-52. [PMID: 26727239 PMCID: PMC4755865 DOI: 10.1038/nchembio.1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.
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Affiliation(s)
- Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Lin Huang
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
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37
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Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A 2016; 113:116-21. [PMID: 26699466 PMCID: PMC4711849 DOI: 10.1073/pnas.1517511113] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
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Affiliation(s)
- Xiaojun Xu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Tao Yu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211; Department of Physics, Jianghan University, Wuhan, Hubei 430056, China
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211;
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38
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Vieweger M, Holmstrom ED, Nesbitt DJ. Single-Molecule FRET Reveals Three Conformations for the TLS Domain of Brome Mosaic Virus Genome. Biophys J 2015; 109:2625-2636. [PMID: 26682819 PMCID: PMC4699858 DOI: 10.1016/j.bpj.2015.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 12/28/2022] Open
Abstract
Metabolite-dependent conformational switching in RNA riboswitches is now widely accepted as a critical regulatory mechanism for gene expression in bacterial systems. More recently, similar gene regulation mechanisms have been found to be important for viral systems as well. One of the most abundant and best-studied systems is the tRNA-like structure (TLS) domain, which has been found to occur in many plant viruses spread across numerous genera. In this work, folding dynamics for the TLS domain of Brome Mosaic Virus have been investigated using single-molecule fluorescence resonance energy transfer techniques. In particular, burst fluorescence methods are exploited to observe metal-ion ([M(n+)])-induced folding in freely diffusing RNA constructs resembling the minimal TLS element of brome mosaic virus RNA3. The results of these experiments reveal a complex equilibrium of at least three distinct populations. A stepwise, or consecutive, thermodynamic model for TLS folding is developed, which is in good agreement with the [M(n+)]-dependent evolution of conformational populations and existing structural information in the literature. Specifically, this folding pathway explains the metal-ion dependent formation of a functional TLS domain from unfolded RNAs via two consecutive steps: 1) hybridization of a long-range stem interaction, followed by 2) formation of a 3'-terminal pseudoknot. These two conformational transitions are well described by stepwise dissociation constants for [Mg(2+)] (K1 = 328 ± 30 μM and K2 = 1092 ± 183 μM) and [Na(+)] (K1 = 74 ± 6 mM and K2 = 243 ± 52 mM)-induced folding. The proposed thermodynamic model is further supported by inhibition studies of the long-range stem interaction using a complementary DNA oligomer, which effectively shifts the dynamic equilibrium toward the unfolded conformation. Implications of this multistep conformational folding mechanism are discussed with regard to regulation of virus replication.
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Affiliation(s)
- Mario Vieweger
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Erik D Holmstrom
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - David J Nesbitt
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado.
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39
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Wang G, Chang X, Peng J, Liu K, Zhao K, Yu C, Fang Y. Towards a new FRET system via combination of pyrene and perylene bisimide: synthesis, self-assembly and fluorescence behavior. Phys Chem Chem Phys 2015; 17:5441-9. [PMID: 25615443 DOI: 10.1039/c4cp04860a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A new fluorescent derivative of cholesterol, N,N'-(N-(2-(3β-cholest-5-en-3yl-formamido)ethyl) pyrene-1-sulfonamido)ethyl perylene-3,4:9,10-tetracarboxylic acid bisimide (CPPBI), was designed and synthesized. In the design, pyrene (Py) and perylene bisimide (PBI) were specially chosen as the energy donor and the acceptor, respectively. Fluorescence studies revealed that (1) CPPBI shows a strong tendency to form supra-molecular assemblies, (2) the assemblies possess a high efficiency of fluorescence resonance energy transfer (FRET) via intermolecular interactions, and (3) the profile and position of its fluorescence emission are highly dependent upon the nature of its medium, but the medium shows little effect on the efficiency of the energy transfer, suggesting that the chromophores including both Py and PBI units enjoy some rotational and/or translational mobility in the aggregated state of the compound. Temperature- and concentration-dependent (1)H NMR spectroscopy studies revealed that both hydrogen-bonding and π-π stacking play a great role in stabilizing the assemblies of the compound, and confirmed the existence of π-π stacking between the Py moieties and between the PBI residues of the compound, of which the donor and the acceptor may have arranged in an appropriate orientation and at a suitable distance which are the key factors to determine the FRET efficiency. Moreover, the CPPBI-based film possesses unusual photochemical stability, and its emission is sensitive to the presence of some organic vapors, in particular aniline.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, P. R. China.
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40
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Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method. Biomech Model Mechanobiol 2015; 15:317-29. [DOI: 10.1007/s10237-015-0690-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/30/2015] [Indexed: 01/14/2023]
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41
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Gamalinda M, Woolford JL. Paradigms of ribosome synthesis: Lessons learned from ribosomal proteins. ACTA ACUST UNITED AC 2015; 3:e975018. [PMID: 26779413 DOI: 10.4161/21690731.2014.975018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/29/2014] [Accepted: 10/06/2014] [Indexed: 12/11/2022]
Abstract
The proteome in all cells is manufactured via the intricate process of translation by multimolecular factories called ribosomes. Nevertheless, these ribonucleoprotein particles, the largest of their kind, also have an elaborate assembly line of their own. Groundbreaking discoveries that bacterial ribosomal subunits can be self-assembled in vitro jumpstarted studies on how ribosomes are constructed. Until recently, ribosome assembly has been investigated almost entirely in vitro with bacterial small subunits under equilibrium conditions. In light of high-resolution ribosome structures and a more sophisticated toolkit, the past decade has been defined by a burst of kinetic studies in vitro and, importantly, also a shift to examining ribosome maturation in living cells, especially in eukaryotes. In this review, we summarize the principles governing ribosome assembly that emerged from studies focusing on ribosomal proteins and their interactions with rRNA. Understanding these paradigms has taken center stage, given the linkage between anomalous ribosome biogenesis and proliferative disorders.
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Affiliation(s)
- Michael Gamalinda
- Department of Biological Sciences; Carnegie Mellon University; Pittsburgh, PA USA; Present Address: Department of Epigenetics; Max Planck Institute of Immunobiology and Epigenetics; Freiburg, Germany
| | - John L Woolford
- Department of Biological Sciences; Carnegie Mellon University ; Pittsburgh, PA USA
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42
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Lu M, Lu HP. Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy. J Phys Chem B 2014; 118:11943-55. [PMID: 25222115 PMCID: PMC4199541 DOI: 10.1021/jp5081498] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Conformational motions of proteins
are highly dynamic and intrinsically
complex. To capture the temporal and spatial complexity of conformational
motions and further to understand their roles in protein functions,
an attempt is made to probe multidimensional conformational dynamics
of proteins besides the typical one-dimensional FRET coordinate or
the projected conformational motions on the one-dimensional FRET coordinate.
T4 lysozyme hinge-bending motions between two domains along α-helix
have been probed by single-molecule FRET. Nevertheless, the domain
motions of T4 lysozyme are rather complex involving multiple coupled
nuclear coordinates and most likely contain motions besides hinge-bending.
It is highly likely that the multiple dimensional protein conformational
motions beyond the typical enzymatic hinged-bending motions have profound
impact on overall enzymatic functions. In this report, we have developed
a single-molecule multiparameter photon stamping spectroscopy integrating
fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic
approach enables simultaneous observations of both FRET-related site-to-site
conformational dynamics and molecular rotational (or orientational)
motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have
further observed wide-distributed rotational flexibility along orientation
coordinates by recording fluorescence anisotropy and simultaneously
identified multiple intermediate conformational states along FRET
coordinate by monitoring time-dependent donor lifetime, presenting
a whole picture of multidimensional conformational dynamics in the
process of T4 lysozyme open-close hinge-bending enzymatic turnover
motions under enzymatic reaction conditions. By analyzing the autocorrelation
functions of both lifetime and anisotropy trajectories, we have also
observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional
conformational fluctuation dynamics, providing a fundamental understanding
of the enzymatic reaction turnover dynamics associated with overall
enzyme as well as the specific active-site conformational fluctuations
that are not identifiable and resolvable in the conventional ensemble-averaged
experiment.
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Affiliation(s)
- Maolin Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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43
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Prevo B, Peterman EJG. Förster resonance energy transfer and kinesin motor proteins. Chem Soc Rev 2014; 43:1144-55. [PMID: 24071719 DOI: 10.1039/c3cs60292c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Förster Resonance Energy Transfer (FRET) is the phenomenon of non-radiative transfer of electronic excitations from a donor fluorophore to an acceptor, mediated by electronic dipole-dipole coupling. The transfer rate and, as a consequence, efficiency depend non-linearly on the distance between the donor and the acceptor. FRET efficiency can thus be used as an effective and accurate reporter of distance between two fluorophores and changes thereof. Over the last 50 years or so, FRET has been used as a spectroscopic ruler to measure conformations and conformational changes of biomolecules. More recently, FRET has been combined with microscopy, ultimately allowing measurement of FRET between a single donor and a single acceptor pair. In this review, we will explain the physical foundations of FRET and how FRET can be applied to biomolecules. We will highlight the power of the different FRET approaches by focusing on its application to the motor protein kinesin, which undergoes several conformational changes driven by enzymatic action, that ultimately result in unidirectional motion along microtubule filaments, driving active transport in the cell. Single-molecule and ensemble FRET studies of different aspects of kinesin have provided numerous insights into the complex chemomechanical mechanism of this fascinating protein.
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Affiliation(s)
- Bram Prevo
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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Dittmore A, Landy J, Molzon AA, Saleh OA. Single-molecule methods for ligand counting: linking ion uptake to DNA hairpin folding. J Am Chem Soc 2014; 136:5974-80. [PMID: 24694039 DOI: 10.1021/ja500094z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ligand associations play a significant role in biochemical processes, typically through stabilizing a particular conformation of a folded biomolecule. Here, we demonstrate the ability to measure the changes in the number of ligands associated with a single, stretched biomolecule as it undergoes a conformational change. We do this by combining thermodynamic theory with single-molecule measurements that directly track biomolecular conformation. We utilize this technique to determine the changes in the ionic atmosphere of a DNA hairpin undergoing a force-destabilized folding transition. We find that the number of counterions liberated upon DNA unfolding is a nonmonotonic function of the monovalent salt concentration of the solution, contrary to predictions from common nucleic acid models. This demonstrates that previously unobserved phenomena can be measured with our ligand counting approach.
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Affiliation(s)
- Andrew Dittmore
- Materials Department and ‡BMSE Program, University of California , Santa Barbara, California 93106, United States
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Abstract
This protocol covers the steps required to incorporate N-hydroxysuccinamide (NHS) functionalized fluorophores into synthetic RNAs containing a residue derivatized with a primary amine. This method has been widely used to label RNA oligonucleotides that are used directly, targeted to a complementary RNA using base pairing rules, or covalently ligated to a RNA of interest (Ha et al., 1999; Hodak et al., 2005; Baum and Silverman, 2007; Sattint et al., 2008; Akiyama and Stone, 2009; Solomatin and Herschlag, 2009). While this technique is quite general, the details of a particular experiment can vary, therefore, it is always important to keep in mind that other labeling strategies are available and should potentially be considered.
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Affiliation(s)
- Max Greenfeld
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA
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Protein-guided RNA dynamics during early ribosome assembly. Nature 2014; 506:334-8. [PMID: 24522531 PMCID: PMC3968076 DOI: 10.1038/nature13039] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/20/2014] [Indexed: 01/30/2023]
Abstract
The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the rRNA structure so that later proteins may join the complex is poorly understood. Here we use single molecule fluorescence resonance energy transfer (smFRET) to observe real-time encounters between ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4-RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free energy path to protein-RNA recognition. Three-color FRET and molecular dynamics (MD) simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. This protein-guided dynamics offers an alternative explanation for induced fit in RNA-protein complexes.
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Lin YC, Lin BL, Setiawan T, Chang CC, Yen CF, Chang WH. A Single Molecule FRET Study of Formation of RNA Polymerase II Elongation Complex on Passivated Surface. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gholami S, Kompany-Zareh M. Multiway study of hybridization in nanoscale semiconductor labeled DNA based on fluorescence resonance energy transfer. Phys Chem Chem Phys 2013; 15:14405-13. [PMID: 23884154 DOI: 10.1039/c3cp51509e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The resolution of the ternary-binary complex competition of a target sequence and of its two complementary probes in sandwich DNA hybridization is reported. To achieve this goal, Fluorescence Resonance Energy Transfer (FRET) between oligonucleotide-functionalized quantum dot (QD) nanoprobes (QD donor-QD acceptor) upon hybridization with a label free target was monitored by two-dimensional photoluminescence excitation spectroscopy (2D-PLE). Detection of a target oligonucleotide strand, using sandwiched nanoassembly in a separation-free format, was performed with the appearance of a new feature in the photoluminescence excitation (PLE) plot. From the obtained data, energy transfer efficiency and Förster radius (R0) were calculated. In particular, our results demonstrated that energy transfer by using QD donor-QD acceptor FRET pairs is more efficient in comparison with QD donor-organic dye acceptor pairs. Soft and model based analysis of 2D-PLE data was implemented by means of PARAFAC and hard trilinear decomposition (HTD), allowing to fit a proper model for FRET-based sandwich DNA hybridization systems. This study is the first successful application of a multiway chemometric technique to consider FRET based DNA hybridization in sandwiched nanoassemblies. A multi-equilibria model was properly fitted to the data and confirmed there is a competition between ternary and binary complex formation. Equilibrium constants of DNA hybridization in sandwiched nanoassemblies were estimated for the first time. Equilibrium constants illustrated that the extent of hybridization in one side on the target strand depends on hybridization conditions on the other side of the strand. Effects of guanine (G) and cytosine (C) contents of strands on the extent and rate of hybridization were investigated. In addition to equilibrium constants of binary and ternary complexes, the pure profiles of all resolved structures were estimated. Ultimately, the described method calculated the analytical concentration of probes as a measure of surface modification yield with DNA using nonlinear fit analysis, without using any calibration sample.
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Affiliation(s)
- Somayeh Gholami
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
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Milas P, Gamari BD, Parrot L, Krueger BP, Rahmanseresht S, Moore J, Goldner LS. Indocyanine dyes approach free rotation at the 3' terminus of A-RNA: a comparison with the 5' terminus and consequences for fluorescence resonance energy transfer. J Phys Chem B 2013; 117:8649-58. [PMID: 23799279 DOI: 10.1021/jp311071y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyanine dyes are widely used to study the folding and structural transformations of nucleic acids using fluorescence resonance energy transfer (FRET). The extent to which FRET can be used to extract inter- and intramolecular distances has been the subject of considerable debate in the literature; the contribution of dye and linker dynamics to the observed FRET signal is particularly troublesome. We used molecular dynamics (MD) simulations to study the dynamics of the indocarbocyanine dyes Cy3 and Cy5 attached variously to the 3' or 5' terminal bases of a 16-base-pair RNA duplex. We then used Monte Carlo modeling of dye photophysics to predict the results of single-molecule-sensitive FRET measurements of these same molecules. Our results show that the average value of FRET depends on both the terminal base and the linker position. In particular, 3' attached dyes typically explore a wide region of configuration space, and the relative orientation factor, κ(2), has a distribution that approaches that of free-rotators. This is in contrast to 5' attached dyes, which spend a significant fraction of their time in one or more configurations that are effectively stacked on the ends of the RNA duplex. The presence of distinct dye configurations for 5' attached dyes is consistent with observations, made by others, of multiple fluorescence lifetimes of Cy3 on nucleic acids. Although FRET is frequently used as a molecular "ruler" to measure intramolecular distances, the unambiguous measurement of distances typically relies on the assumption that the rotational degrees of freedom of the dyes can be averaged out and that the donor lifetime in the absence of the acceptor is a constant. We demonstrate that even for the relatively free 3' attached dyes, the correlation time of κ(2) is still too long to justify the use of a free-rotation approximation. We further explore the consequences of multiple donor lifetimes on the predicted value of FRET.
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Affiliation(s)
- Peker Milas
- Department of Physics, University of Massachusetts, Amherst, Amherst, Massachusetts, USA
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Wang L, Wasserman MR, Feldman MB, Altman RB, Blanchard SC. Mechanistic insights into antibiotic action on the ribosome through single-molecule fluorescence imaging. Ann N Y Acad Sci 2013; 1241:E1-16. [PMID: 23419024 DOI: 10.1111/j.1749-6632.2012.06839.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule fluorescence imaging has provided unprecedented access to the dynamics of ribosome function, revealing transient intermediate states that are critical to ribosome activity. Imaging platforms have now been developed that are capable of probing many hundreds of molecules simultaneously at temporal and spatial resolutions approaching the sub-millisecond time and the sub-nanometer scales. These advances enable both steady- and pre-steady state measurements of individual steps in the translation process as well as processive reactions. The data generated using these methods have yielded new, quantitative structural and kinetic insights into ribosomal activity. They have also shed light on the mechanisms of antibiotic targeting the translation apparatus, revealing features of the structure-function relationship that would be difficult to obtain by other means. This review provides an overview of the types of information that can be obtained using such imaging platforms and a blueprint for using the technique to assess how small-molecule antibiotics alter macromolecular functions.
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Affiliation(s)
- Leyi Wang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
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