1
|
Meyer J, Payr M, Duss O, Hennig J. Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression. Biochem Soc Trans 2024; 52:2267-2279. [PMID: 39601754 DOI: 10.1042/bst20231240] [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: 06/12/2024] [Revised: 10/14/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024]
Abstract
Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.
Collapse
Affiliation(s)
- Julia Meyer
- Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marco Payr
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Candidate for Joint PhD Degree From EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Olivier Duss
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Janosch Hennig
- Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| |
Collapse
|
2
|
Stubhan S, Baptist AV, Körösy C, Narducci A, Moya Muñoz GG, Wendler N, Lak A, Sztucki M, Cordes T, Lipfert J. Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry. NANOSCALE 2024. [PMID: 39691975 DOI: 10.1039/d4nr03375b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
Abstract
Biomolecular structures are typically determined using frozen or crystalline samples. Measurement of intramolecular distances in solution can provide additional insights into conformational heterogeneity and dynamics of biological macromolecules and their complexes. The established molecular ruler techniques used for this (NMR, FRET, and EPR) are, however, limited in their dynamic range and require model assumptions to determine absolute distance or distance distributions. Here, we introduce anomalous X-ray scattering interferometry (AXSI) for intramolecular distance measurements in proteins, which are labeled at two sites with small gold nanoparticles of 0.7 nm radius. We apply AXSI to two different cysteine-variants of maltose binding protein in the presence and absence of its ligand maltose and find distances in quantitative agreement with single-molecule FRET experiments. Our study shows that AXSI enables determination of intramolecular distance distributions under virtually arbitrary solution conditions and we anticipate its broad use to characterize protein conformational ensembles and dynamics.
Collapse
Affiliation(s)
- Samuel Stubhan
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands.
| | - Anna V Baptist
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Caroline Körösy
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands.
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Gustavo Gabriel Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Aidin Lak
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | | | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
- Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Jan Lipfert
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands.
- Institute for Physics, Augsburg University, Universitätsstrasse 1, 86159 Augsburg, Germany
| |
Collapse
|
3
|
Kayyil Veedu M, Lavilley G, Sy M, Goetz J, Charbonnière LJ, Wenger J. Watching lanthanide nanoparticles one at a time: characterization of their photoluminescence dynamics at the single nanoparticle level. NANOSCALE 2024. [PMID: 39688266 DOI: 10.1039/d4nr02988g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
Lanthanide nanoparticles (LnNPs) feature sharp emission lines together with millisecond emission lifetimes which make them promising luminescent probes for biosensing and bioimaging. Although LnNPs are attracting much interest, their photoluminescence properties at the single nanoparticle level remain largely unexplored. Here, we employ fluorescence correlation spectroscopy (FCS) and photoluminescence burst analysis to investigate the photodynamics of Sm- and Eu-based LnNPs with single nanoparticle sensitivity and microsecond resolution. By recording the photoluminescence intensity and the number of contributing LnNPs, we compute the photoluminescence brightness per individual nanoparticle and estimate the actual number of emitting centers per nanoparticle. Our approach overcomes the challenges associated with ensemble-averaged techniques and provides insights into LnNP photodynamics. Moreover, we demonstrate our microscope's ability to detect and analyze LnNPs at the single nanoparticle level, monitoring both photoluminescence brightness and burst duration. These findings expand our understanding of LnNPs and pave the way for advanced biosensing applications at the single nanoparticle level.
Collapse
Affiliation(s)
- Malavika Kayyil Veedu
- Aix Marseille Univ, CNRS, Centrale Med, Institut Fresnel, AMUTech, 13013 Marseille, France.
| | - Gemma Lavilley
- Poly-Dtech, 204 avenue de Colmar, 67100 Strasbourg, France
- Equipe de Synthèse Pour l'Analyse, Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178 CNRS/University of Strasbourg, Cedex 2, 67087 Strasbourg, France
| | - Mohamadou Sy
- Poly-Dtech, 204 avenue de Colmar, 67100 Strasbourg, France
| | - Joan Goetz
- Poly-Dtech, 204 avenue de Colmar, 67100 Strasbourg, France
| | - Loïc J Charbonnière
- Equipe de Synthèse Pour l'Analyse, Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178 CNRS/University of Strasbourg, Cedex 2, 67087 Strasbourg, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Med, Institut Fresnel, AMUTech, 13013 Marseille, France.
| |
Collapse
|
4
|
Miller JJ, Mallimadugula UL, Zimmerman MI, Stuchell-Brereton MD, Soranno A, Bowman GR. Accounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational States. J Chem Theory Comput 2024; 20:10339-10349. [PMID: 39588651 DOI: 10.1021/acs.jctc.4c01068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
Abstract
Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein's structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a protein's dynamics. This allows us to accurately assess which time scales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (Aβ40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in nuclear magnetic resonance, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings. Understanding protein dynamics is crucial for understanding protein function, yet few methodologies report on protein motion at an atomic level. Combining single molecule Förster resonance energy transfer (smFRET) experiments with computer simulations could provide atomistic models of protein ensembles which are grounded in experiments, however, there has been limited agreement between the two methods to date. Here, we present an algorithm to recapitulate smFRET experiments from molecular dynamics simulations. This approach significantly improves agreement between simulations and experiments for proteins across the ordered spectrum. Moreover, with this approach we can confidently create atomic models for states observed during smFRET experiments which were otherwise difficult to model due to high amounts of flexibility, disorder, or large deviations from crystal-like states.
Collapse
Affiliation(s)
- Justin J Miller
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Upasana L Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Gregory R Bowman
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
5
|
Gao S, Liang J, Tan C, Ma J. An oxygen-scavenging system without impact on DNA mechanical properties in single-molecule fluorescence experiments. NANOSCALE 2024. [PMID: 39633609 DOI: 10.1039/d4nr04287e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Oxygen scavenging systems (OSSs) are critical for dye stability in single-molecule fluorescence (SMF) experiments. However, the commonly used protocatechuic acid (PCA)/protocatechuate-3,4-dioxygenase (PCD) OSS alters DNA mechanical properties, limiting its applicability. To address this limitation, we examine the bilirubin oxidase (BOD) OSS, which had not been previously used in single-molecule experiments, alongside the pyranose oxidase and catalase (POC) OSS. Our results revealed that POC OSS affected DNA mechanics in a buffer-dependent manner, while BOD OSS had no discernible effect across all tested buffer conditions. Furthermore, BOD OSS significantly extended the photobleaching lifetimes of Cy3 and Cy5 dyes and caused minimal pH changes compared to PCD OSS. Collectively, these findings highlight the superior performance of BOD OSS, suggesting its potential for widespread application, particularly in experiments combining SMF with single-molecule force spectroscopy (SMFS) measurements.
Collapse
Affiliation(s)
- Shang Gao
- School of Physics, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China
| | - Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China
| | - Chuang Tan
- School of Physics, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China
| |
Collapse
|
6
|
Ghosh S, Schmid S. The potential of fluorogenicity for single molecule FRET and DyeCycling. QRB DISCOVERY 2024; 5:e8. [PMID: 39687231 PMCID: PMC11649375 DOI: 10.1017/qrd.2024.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 12/18/2024] Open
Abstract
Single Molecule Förster Resonance Energy Transfer (smFRET) is a popular technique to directly observe biomolecular dynamics in real time, offering unique mechanistic insight into proteins, ribozymes, and so forth. However, inevitable photobleaching of the fluorophores puts a stringent limit on the total time a surface-tethered molecule can be monitored, fundamentally limiting the information gain through conventional smFRET measurements. DyeCycling addresses this problem by using reversibly - instead of covalently - coupled FRET fluorophores, through which it can break the photobleaching limit and theoretically provide unlimited observation time. In this perspective paper, we discuss the potential of various fluorogenic strategies to suppress the background fluorescence caused by unbound, freely diffusing fluorophores inherent to the DyeCycling approach. In comparison to nanophotonic background suppression using zero-mode waveguides, the fluorogenic approach would enable DyeCycling experiments on regular glass slides with fluorogenic FRET probes that are quenched in solution and only fluoresce upon target binding. We review a number of fluorogenic approaches and conclude, among other things, that short-range quenching appears promising for realising fluorogenic DyeCycling on regular glass slides. We anticipate that our discussion will be relevant for all single-molecule fluorescence techniques that use reversible fluorophore binding.
Collapse
Affiliation(s)
- Srijayee Ghosh
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Sonja Schmid
- Department of Chemistry, University of Basel, Basel, Switzerland
| |
Collapse
|
7
|
Frost D, Cook K, Sanabria H. Time-heterogeneity of the Förster Radius from Dipole Orientational Dynamics Impacts Single-Molecule FRET Experiments. ARXIV 2024:arXiv:2404.09883v2. [PMID: 38699162 PMCID: PMC11065046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Förster resonance energy transfer (FRET) is a quantum mechanical phenomenon involving the non-radiative transfer of energy between coupled electric dipoles. Due to the strong dependence of FRET on the distance between the dipoles, it is frequently used as a "molecular ruler" in biology, chemistry, and physics. This is done by placing dipolar molecules called dyes on molecules of interest. In time-resolved confocal single-molecule FRET (smFRET) experiments, the joint distribution of the FRET efficiency and the donor fluorescence lifetime can reveal underlying molecular conformational dynamics via deviation from their theoretical Förster relationship. This deviation is referred to as a dynamic shift. Quantifying the dynamic shift caused by the motion of the fluorescent dyes is essential to decoupling the dynamics of the studied molecules and the dyes. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based on first principle physics and proper dye linker chemistry to match accessible volumes predicted by molecular dynamics simulations. By simulating the dyes' stochastic translational and rotational dynamics, we show that the observed dynamic shift can largely be attributed to the mutual orientational dynamics of the electric dipole moments associated with the dyes, not their accessible volume. Our models provide the most up-to-date and accurate estimation of FRET.
Collapse
Affiliation(s)
- David Frost
- School of Mathematical and Statistical Sciences, Clemson University
| | - Keisha Cook
- School of Mathematical and Statistical Sciences, Clemson University
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University
| |
Collapse
|
8
|
Berg A, Velayuthan LP, Tågerud S, Ušaj M, Månsson A. Probing actin-activated ATP turnover kinetics of human cardiac myosin II by single molecule fluorescence. Cytoskeleton (Hoboken) 2024; 81:883-901. [PMID: 38623952 PMCID: PMC11615843 DOI: 10.1002/cm.21858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Mechanistic insights into myosin II energy transduction in striated muscle in health and disease would benefit from functional studies of a wide range of point-mutants. This approach is, however, hampered by the slow turnaround of myosin II expression that usually relies on adenoviruses for gene transfer. A recently developed virus-free method is more time effective but would yield too small amounts of myosin for standard biochemical analyses. However, if the fluorescent adenosine triphosphate (ATP) and single molecule (sm) total internal reflection fluorescence microscopy previously used to analyze basal ATP turnover by myosin alone, can be expanded to actin-activated ATP turnover, it would appreciably reduce the required amount of myosin. To that end, we here describe zero-length cross-linking of human cardiac myosin II motor fragments (sub-fragment 1 long [S1L]) to surface-immobilized actin filaments in a configuration with maintained actin-activated ATP turnover. After optimizing the analysis of sm fluorescence events, we show that the amount of myosin produced from C2C12 cells in one 60 mm cell culture plate is sufficient to obtain both the basal myosin ATP turnover rate and the maximum actin-activated rate constant (k cat). Our analysis of many single binding events of fluorescent ATP to many S1L motor fragments revealed processes reflecting basal and actin-activated ATPase, but also a third exponential process consistent with non-specific ATP-binding outside the active site.
Collapse
Affiliation(s)
- Albin Berg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life ScienceLinnaeus UniversityKalmarSweden
| | - Lok Priya Velayuthan
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life ScienceLinnaeus UniversityKalmarSweden
| | - Sven Tågerud
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life ScienceLinnaeus UniversityKalmarSweden
| | - Marko Ušaj
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life ScienceLinnaeus UniversityKalmarSweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life ScienceLinnaeus UniversityKalmarSweden
| |
Collapse
|
9
|
Hanke CA, Westbrook JD, Webb BM, Peulen TO, Lawson CL, Sali A, Berman HM, Seidel CAM, Vallat B. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Methods 2024; 21:1970-1972. [PMID: 39349602 DOI: 10.1038/s41592-024-02428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Affiliation(s)
- Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Benjamin M Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
| | - Thomas-O Peulen
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
- Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
10
|
Zhou S, Miao Y, Qiu H, Yao Y, Wang W, Chen C. Deep learning based local feature classification to automatically identify single molecule fluorescence events. Commun Biol 2024; 7:1404. [PMID: 39468368 PMCID: PMC11519536 DOI: 10.1038/s42003-024-07122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 10/22/2024] [Indexed: 10/30/2024] Open
Abstract
Long-term single-molecule fluorescence measurements are widely used powerful tools to study the conformational dynamics of biomolecules in real time to further elucidate their conformational dynamics. Typically, thousands or even more single-molecule traces are analyzed to provide statistically meaningful information, which is labor-intensive and can introduce user bias. Recently, several deep-learning models have been developed to automatically classify single-molecule traces. In this study, we introduce DEBRIS (Deep lEarning Based fRagmentatIon approach for Single-molecule fluorescence event identification), a deep-learning model focusing on classifying local features and capable of automatically identifying steady fluorescence signals and dynamically emerging signals of different patterns. DEBRIS efficiently and accurately identifies both one-color and two-color single-molecule events, including their start and end points. By adjusting user-defined criteria, DEBRIS becomes the pioneer in using a deep learning model to accurately classify four different types of single-molecule fluorescence events using the same trained model, demonstrating its universality and ability to enrich the current toolbox.
Collapse
Affiliation(s)
- Shuqi Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yu Miao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Haoren Qiu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuan Yao
- Department of Mathematics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wenjuan Wang
- Technology Center for Protein Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
| |
Collapse
|
11
|
Li J, Zhang L, Johnson-Buck A, Walter NG. Foundation model for efficient biological discovery in single-molecule data. RESEARCH SQUARE 2024:rs.3.rs-4970585. [PMID: 39483892 PMCID: PMC11527229 DOI: 10.21203/rs.3.rs-4970585/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Modern data-intensive techniques offer ever deeper insights into biology, but render the process of discovery increasingly complex. For example, exploiting the unique ability of single-molecule fluorescence microscopy (SMFM)1-5. to uncover rare but critical intermediates often demands manual inspection of time traces and iterative ad hoc approaches that are difficult to systematize. To facilitate systematic and efficient discovery from SMFM data, we introduce META-SiM, a transformer-based foundation model pre-trained on diverse SMFM analysis tasks. META-SiM achieves high performance-rivaling best-in-class algorithms-on a broad range of analysis tasks including trace selection, classification, segmentation, idealization, and stepwise photobleaching analysis. Additionally, the model produces high-dimensional embedding vectors that encapsulate detailed information about each trace, which the web-based META-SiM Projector (https://www.simol-projector.org) casts into lower-dimensional space for efficient whole-dataset visualization, labeling, comparison, and sharing. Combining this Projector with the objective metric of Local Shannon Entropy enables rapid identification of condition-specific behaviors, even if rare or subtle. As a result, by applying META-SiM to an existing single-molecule Förster resonance energy transfer (smFRET) dataset6, we discover a previously unobserved intermediate state in pre-mRNA splicing. META-SiM thus removes bottlenecks, improves objectivity, and both systematizes and accelerates biological discovery in complex single-molecule data.
Collapse
Affiliation(s)
- Jieming Li
- Bristol Myers Squibb, New Brunswick, NJ, USA
| | | | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
12
|
Zhang YM, Li B, Wu WQ. Single-molecule insights into repetitive helicases. J Biol Chem 2024; 300:107894. [PMID: 39424144 PMCID: PMC11603008 DOI: 10.1016/j.jbc.2024.107894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024] Open
Abstract
Helicases are ubiquitous motors involved in almost all aspects of nucleic acid metabolism; therefore, revealing their unwinding behaviors and mechanisms is fundamentally and medically essential. In recent decades, single-molecule applications have revolutionized our ability to study helicases by avoiding the averaging of bulk assays and bridging the knowledge gap between dynamics and structures. This advancement has updated our understanding of the biochemical properties of helicases, such as their rate, directionality, processivity, and step size, while also uncovering unprecedented mechanistic insights. Among these, repetitive motion, a new feature of helicases, is one of the most remarkable discoveries. However, comprehensive reviews and comparisons are still lacking. Consequently, the present review aims to summarize repetitive helicases, compare the repetitive phenomena, and discuss the underlying molecular mechanisms. This review may provide a systematic understanding of repetitive helicases and help understand their cellular functions.
Collapse
Affiliation(s)
- Ya-Mei Zhang
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Alzheimer's Disease, Henan University, Kaifeng, China
| | - Bo Li
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Alzheimer's Disease, Henan University, Kaifeng, China
| | - Wen-Qiang Wu
- School of Nursing and Health, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng Key Laboratory Active Prevention and Nursing of Alzheimer's Disease, Henan University, Kaifeng, China.
| |
Collapse
|
13
|
Moya Muñoz GG, Brix O, Klocke P, Harris PD, Luna Piedra JR, Wendler ND, Lerner E, Zijlstra N, Cordes T. Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC). SCIENCE ADVANCES 2024; 10:eado3427. [PMID: 39321299 PMCID: PMC11423890 DOI: 10.1126/sciadv.ado3427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
Abstract
Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is, however, a growing gap between the state of the art and what is accessible to biologists, biochemists, medical researchers, or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed microspectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy, time-correlated single-photon counting and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines, are provided, to allow non-optics specialists to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and open-source Brick-MIC platform will be a valuable tool for many laboratories worldwide.
Collapse
Affiliation(s)
- Gabriel G. Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Philipp Klocke
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul D. Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jorge R. Luna Piedra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Nicolas D. Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| |
Collapse
|
14
|
Verma AR, Ray KK, Bodick M, Kinz-Thompson CD, Gonzalez RL. Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophys J 2024; 123:2765-2780. [PMID: 38268189 PMCID: PMC11393709 DOI: 10.1016/j.bpj.2024.01.022] [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: 08/15/2023] [Revised: 11/28/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
Time-dependent single-molecule experiments contain rich kinetic information about the functional dynamics of biomolecules. A key step in extracting this information is the application of kinetic models, such as hidden Markov models (HMMs), which characterize the molecular mechanism governing the experimental system. Unfortunately, researchers rarely know the physicochemical details of this molecular mechanism a priori, which raises questions about how to select the most appropriate kinetic model for a given single-molecule data set and what consequences arise if the wrong model is chosen. To address these questions, we have developed and used time-series modeling, analysis, and visualization environment (tMAVEN), a comprehensive, open-source, and extensible software platform. tMAVEN can perform each step of the single-molecule analysis pipeline, from preprocessing to kinetic modeling to plotting, and has been designed to enable the analysis of a single-molecule data set with multiple types of kinetic models. Using tMAVEN, we have systematically investigated mismatches between kinetic models and molecular mechanisms by analyzing simulated examples of prototypical single-molecule data sets exhibiting common experimental complications, such as molecular heterogeneity, with a series of different types of HMMs. Our results show that no single kinetic modeling strategy is mathematically appropriate for all experimental contexts. Indeed, HMMs only correctly capture the underlying molecular mechanism in the simplest of cases. As such, researchers must modify HMMs using physicochemical principles to avoid the risk of missing the significant biological and biophysical insights into molecular heterogeneity that their experiments provide. By enabling the facile, side-by-side application of multiple types of kinetic models to individual single-molecule data sets, tMAVEN allows researchers to carefully tailor their modeling approach to match the complexity of the underlying biomolecular dynamics and increase the accuracy of their single-molecule data analyses.
Collapse
Affiliation(s)
- Anjali R Verma
- Department of Chemistry, Columbia University, New York, New York
| | - Korak Kumar Ray
- Department of Chemistry, Columbia University, New York, New York
| | - Maya Bodick
- Department of Chemistry, Columbia University, New York, New York
| | | | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York.
| |
Collapse
|
15
|
Asadiatouei P, Salem CB, Wanninger S, Ploetz E, Lamb DC. Deep-LASI, single-molecule data analysis software. Biophys J 2024; 123:2682-2695. [PMID: 38384132 PMCID: PMC11393668 DOI: 10.1016/j.bpj.2024.02.013] [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: 11/30/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
By avoiding ensemble averaging, single-molecule methods provide novel means of extracting mechanistic insights into function of material and molecules at the nanoscale. However, one of the big limitations is the vast amount of data required for analyzing and extracting the desired information, which is time-consuming and user dependent. Here, we introduce Deep-LASI, a software suite for the manual and automatic analysis of single-molecule traces, interactions, and the underlying kinetics. The software can handle data from one-, two- and three-color fluorescence data, and was particularly designed for the analysis of two- and three-color single-molecule fluorescence resonance energy transfer experiments. The functionalities of the software include: the registration of multiple-channels, trace sorting and categorization, determination of the photobleaching steps, calculation of fluorescence resonance energy transfer correction factors, and kinetic analyses based on hidden Markov modeling or deep neural networks. After a kinetic analysis, the ensuing transition density plots are generated, which can be used for further quantification of the kinetic parameters of the system. Each step in the workflow can be performed manually or with the support of machine learning algorithms. Upon reading in the initial data set, it is also possible to perform the remaining analysis steps automatically without additional supervision. Hence, the time dedicated to the analysis of single-molecule experiments can be reduced from days/weeks to minutes. After a thorough description of the functionalities of the software, we also demonstrate the capabilities of the software via the analysis of a previously published dynamic three-color DNA origami structure fluctuating between three states. With the drastic time reduction in data analysis, new types of experiments become realistically possible that complement our currently available palette of methodologies for investigating the nanoworld.
Collapse
Affiliation(s)
- Pooyeh Asadiatouei
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens-Bässem Salem
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
| |
Collapse
|
16
|
Bartels N, van der Voort NTM, Opanasyuk O, Felekyan S, Greife A, Shang X, Bister A, Wiek C, Seidel CAM, Monzel C. Advanced multiparametric image spectroscopy and super-resolution microscopy reveal a minimal model of CD95 signal initiation. SCIENCE ADVANCES 2024; 10:eadn3238. [PMID: 39213362 DOI: 10.1126/sciadv.adn3238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Unraveling the concentration-dependent spatiotemporal organization of receptors in the plasma membrane is crucial to understand cell signal initiation. A paradigm of this process is the oligomerization of CD95 during apoptosis signaling, with different oligomerization models being discussed. Here, we establish the molecular-sensitive approach cell lifetime Förster resonance energy transfer image spectroscopy to determine CD95 configurations in live cells. These data are corroborated by stimulated emission depletion microscopy, confocal photobleaching step analysis, and fluorescence correlation spectroscopy. We probed CD95 interactions for concentrations of ~10 to 1000 molecules per square micrometer, over nanoseconds to hours, and molecular to cellular scales. Quantitative benchmarking was achieved establishing high-fidelity monomer and dimer controls. While CD95 alone is primarily monomeric (~96%) and dimeric (4%), the addition of ligand induces oligomerization to dimers/trimers (~15%) leading to cell death. This study highlights molecular concentration effects and oligomerization dynamics. It reveals a minimal model, where small CD95 oligomers suffice to efficiently initiate signaling.
Collapse
Affiliation(s)
- Nina Bartels
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Oleg Opanasyuk
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Suren Felekyan
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Annemarie Greife
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Xiaoyue Shang
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
| | - Arthur Bister
- Department of Otorhinolaryngology, Head & Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology, Head & Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Düsseldorf, Germany
| |
Collapse
|
17
|
Li J, Zhang L, Johnson-Buck A, Walter NG. Foundation model for efficient biological discovery in single-molecule data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609721. [PMID: 39253410 PMCID: PMC11383305 DOI: 10.1101/2024.08.26.609721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Modern data-intensive techniques offer ever deeper insights into biology, but render the process of discovery increasingly complex. For example, exploiting the unique ability of single-molecule fluorescence microscopy (SMFM)1-5. to uncover rare but critical intermediates often demands manual inspection of time traces and iterative ad hoc approaches that are difficult to systematize. To facilitate systematic and efficient discovery from SMFM data, we introduce META-SiM, a transformer-based foundation model pre-trained on diverse SMFM analysis tasks. META-SiM achieves high performance-rivaling best-in-class algorithms-on a broad range of analysis tasks including trace selection, classification, segmentation, idealization, and stepwise photobleaching analysis. Additionally, the model produces high-dimensional embedding vectors that encapsulate detailed information about each trace, which the web-based META-SiM Projector (https://www.simol-projector.org) casts into lower-dimensional space for efficient whole-dataset visualization, labeling, comparison, and sharing. Combining this Projector with the objective metric of Local Shannon Entropy enables rapid identification of condition-specific behaviors, even if rare or subtle. As a result, by applying META-SiM to an existing single-molecule Förster resonance energy transfer (smFRET) dataset6, we discover a previously unobserved intermediate state in pre-mRNA splicing. META-SiM thus removes bottlenecks, improves objectivity, and both systematizes and accelerates biological discovery in complex single-molecule data.
Collapse
Affiliation(s)
- Jieming Li
- Bristol Myers Squibb, New Brunswick, NJ, USA
| | | | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
18
|
Bleier J, Furtado de Mendonca PR, Habrian CH, Stanley C, Vyklicky V, Isacoff EY. Subtype-specific conformational landscape of NMDA receptor gating. Cell Rep 2024; 43:114634. [PMID: 39154344 PMCID: PMC11446236 DOI: 10.1016/j.celrep.2024.114634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/22/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
N-methyl-D-aspartate receptors are ionotropic glutamate receptors that mediate synaptic transmission and plasticity. Variable GluN2 subunits in diheterotetrameric receptors with identical GluN1 subunits set very different functional properties. To understand this diversity, we use single-molecule fluorescence resonance energy transfer (smFRET) to measure the conformations of the ligand binding domain and modulatory amino-terminal domain of the common GluN1 subunit in receptors with different GluN2 subunits. Our results demonstrate a strong influence of the GluN2 subunits on GluN1 rearrangements, both in non-agonized and partially agonized activation intermediates, which have been elusive to structural analysis, and in the fully liganded state. Chimeric analysis reveals structural determinants that contribute to these subtype differences. Our study provides a framework for understanding the conformational landscape that supports highly divergent levels of activity, desensitization, and agonist potency in receptors with different GluN2s and could open avenues for the development of subtype-specific modulators.
Collapse
Affiliation(s)
- Julia Bleier
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Chris H Habrian
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cherise Stanley
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vojtech Vyklicky
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ehud Y Isacoff
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Weill Neurohub, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biology & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
19
|
Steffen FD, Cunha RA, Sigel RKO, Börner R. FRET-guided modeling of nucleic acids. Nucleic Acids Res 2024; 52:e59. [PMID: 38869063 PMCID: PMC11260485 DOI: 10.1093/nar/gkae496] [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: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
The functional diversity of RNAs is encoded in their innate conformational heterogeneity. The combination of single-molecule spectroscopy and computational modeling offers new attractive opportunities to map structural transitions within nucleic acid ensembles. Here, we describe a framework to harmonize single-molecule Förster resonance energy transfer (FRET) measurements with molecular dynamics simulations and de novo structure prediction. Using either all-atom or implicit fluorophore modeling, we recreate FRET experiments in silico, visualize the underlying structural dynamics and quantify the reaction coordinates. Using multiple accessible-contact volumes as a post hoc scoring method for fragment assembly in Rosetta, we demonstrate that FRET can be used to filter a de novo RNA structure prediction ensemble by refuting models that are not compatible with in vitro FRET measurement. We benchmark our FRET-assisted modeling approach on double-labeled DNA strands and validate it against an intrinsically dynamic manganese(II)-binding riboswitch. We show that a FRET coordinate describing the assembly of a four-way junction allows our pipeline to recapitulate the global fold of the riboswitch displayed by the crystal structure. We conclude that computational fluorescence spectroscopy facilitates the interpretability of dynamic structural ensembles and improves the mechanistic understanding of nucleic acid interactions.
Collapse
Affiliation(s)
- Fabio D Steffen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard A Cunha
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
20
|
Dhar M, Berg MA. Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Photon and photon-counting noise. J Chem Phys 2024; 161:034116. [PMID: 39028845 DOI: 10.1063/5.0212157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/28/2024] [Indexed: 07/21/2024] Open
Abstract
A preceding paper [M. Dhar, J. A. Dickinson, and M. A. Berg, J. Chem. Phys. 159, 054110 (2023)] shows how to remove additive noise from an experimental time series, allowing both the equilibrium distribution of the system and its Green's function to be recovered. The approach is based on nonlinear-correlation functions and is fully nonparametric: no initial model of the system or of the noise is needed. However, single-molecule spectroscopy often produces time series with either photon or photon-counting noise. Unlike additive noise, photon noise is signal-size correlated and quantized. Photon counting adds the potential for bias. This paper extends noise-corrected-correlation methods to these cases and tests them on synthetic datasets. Neither signal-size correlation nor quantization is a significant complication. Analysis of the sampling error yields guidelines for the data quality needed to recover the properties of a system with a given complexity. We show that bias in photon-counting data can be corrected, even at the high count rates needed to optimize the time resolution. Using all these results, we discuss the factors that limit the time resolution of single-molecule spectroscopy and the conditions that would be needed to push measurements into the submicrosecond region.
Collapse
Affiliation(s)
- Mainak Dhar
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Mark A Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| |
Collapse
|
21
|
Joshi B, de Lannoy C, Howarth MR, Kim SH, Joo C. iMAX FRET (Information Maximized FRET) for Multipoint Single-Molecule Structural Analysis. NANO LETTERS 2024; 24:8487-8494. [PMID: 38975639 PMCID: PMC11261617 DOI: 10.1021/acs.nanolett.4c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Understanding the structure of biomolecules is vital for deciphering their roles in biological systems. Single-molecule techniques have emerged as alternatives to conventional ensemble structure analysis methods for uncovering new biology in molecular dynamics and interaction studies, yet only limited structural information could be obtained experimentally. Here, we address this challenge by introducing iMAX FRET, a one-pot method that allows ab initio 3D profiling of individual molecules using two-color FRET measurements. Through the stochastic exchange of fluorescent weak binders, iMAX FRET simultaneously assesses multiple distances on a biomolecule within a few minutes, which can then be used to reconstruct the coordinates of up to four points in each molecule, allowing structure-based inference. We demonstrate the 3D reconstruction of DNA nanostructures, protein quaternary structures, and conformational changes in proteins. With iMAX FRET, we provide a powerful approach to advance the understanding of biomolecular structure by expanding conventional FRET analysis to three dimensions.
Collapse
Affiliation(s)
- Bhagyashree
S. Joshi
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Carlos de Lannoy
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Mark R. Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Sung Hyun Kim
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
- Department
of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
- New
and Renewable Energy Research Center, Ewha
Womans University, Seoul 03760, Republic
of Korea
| | - Chirlmin Joo
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
- Department
of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
| |
Collapse
|
22
|
Moya Muñoz GG, Brix O, Klocke P, Harris PD, Luna Piedra JR, Wendler ND, Lerner E, Zijlstra N, Cordes T. Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573596. [PMID: 38234760 PMCID: PMC10793419 DOI: 10.1101/2023.12.29.573596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and opensource Brick-MIC platform will be a valuable tool for many laboratories worldwide.
Collapse
Affiliation(s)
- Gabriel G. Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Philipp Klocke
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Paul D. Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jorge R. Luna Piedra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Nicolas D. Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| |
Collapse
|
23
|
Cichos F, Xia T, Yang H, Zijlstra P. The ever-expanding optics of single-molecules and nanoparticles. J Chem Phys 2024; 161:010401. [PMID: 38949895 DOI: 10.1063/5.0221680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Affiliation(s)
- F Cichos
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - T Xia
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - H Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - P Zijlstra
- Department of Applied Physics and Science Education, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
| |
Collapse
|
24
|
Bogdanova YA, Solovyev ID, Baleeva NS, Myasnyanko IN, Gorshkova AA, Gorbachev DA, Gilvanov AR, Goncharuk SA, Goncharuk MV, Mineev KS, Arseniev AS, Bogdanov AM, Savitsky AP, Baranov MS. Fluorescence lifetime multiplexing with fluorogen activating protein FAST variants. Commun Biol 2024; 7:799. [PMID: 38956304 PMCID: PMC11219735 DOI: 10.1038/s42003-024-06501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling.
Collapse
Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ilya D Solovyev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Anastasia A Gorshkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Goethe University Frankfurt, Frankfurt am Main, 60433, Germany
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Department of Photonics, İzmir Institute of Technology, 35430, İzmir, Turkey
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, 119991 Russia, 121205, Moscow, Russia.
| |
Collapse
|
25
|
Modak A, Kilic Z, Chattrakun K, Terry DS, Kalathur RC, Blanchard SC. Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. Annu Rev Biophys 2024; 53:427-453. [PMID: 39013028 DOI: 10.1146/annurev-biophys-070323-024308] [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] [Indexed: 07/18/2024]
Abstract
Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.
Collapse
Affiliation(s)
- Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Kanokporn Chattrakun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
26
|
Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [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] [Indexed: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
Collapse
Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
| |
Collapse
|
27
|
Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401150. [PMID: 38582512 PMCID: PMC11220639 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
Collapse
Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325011China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Haihong Li
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
| | - Ximiao Hou
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
| |
Collapse
|
28
|
Pati AK, Kilic Z, Martin MI, Terry DS, Borgia A, Bar S, Jockusch S, Kiselev R, Altman RB, Blanchard SC. Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation. Nat Methods 2024; 21:1222-1230. [PMID: 38877317 PMCID: PMC11239528 DOI: 10.1038/s41592-024-02293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) methods employed to quantify time-dependent compositional and conformational changes within biomolecules require elevated illumination intensities to recover robust photon emission streams from individual fluorophores. Here we show that outside the weak-excitation limit, and in regimes where fluorophores must undergo many rapid cycles of excitation and relaxation, non-fluorescing, excitation-induced triplet states with lifetimes orders of magnitude longer lived than photon-emitting singlet states degrade photon emission streams from both donor and acceptor fluorophores resulting in illumination-intensity-dependent changes in FRET efficiency. These changes are not commonly taken into consideration; therefore, robust strategies to suppress excited state accumulations are required to recover accurate and precise FRET efficiency, and thus distance, estimates. We propose both robust triplet state suppression and data correction strategies that enable the recovery of FRET efficiencies more closely approximating true values, thereby extending the spatial and temporal resolution of smFRET.
Collapse
Affiliation(s)
- Avik K Pati
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maxwell I Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sukanta Bar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steffen Jockusch
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
| | - Roman Kiselev
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Roger B Altman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
29
|
Velasco L, Islam AN, Kundu K, Oi A, Reinhard BM. Two-color interferometric scattering (iSCAT) microscopy reveals structural dynamics in discrete plasmonic molecules. NANOSCALE 2024; 16:11696-11704. [PMID: 38860984 PMCID: PMC11189637 DOI: 10.1039/d4nr01288g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Plasmonic molecules are discrete assemblies of noble metal nanoparticles (NPs) that are of interest as transducers in optical nanosensors. So far, NPs with diameters of ∼40 nm have been the preferred building blocks for plasmonic molecules intended as optical single molecule sensors due to difficulties associated with detecting smaller NPs through elastic scattering in conventional darkfield microscopy. Here, we apply 405 nm, 445 nm two-color interferometric scattering (iSCAT) microscopy to characterize polyethylene glycol (PEG) tethered dimers of 10 nm and 20 nm Ag NPs and their monomers. Dimers of both NP sizes can be discerned from their respective monomers through changes in the average iSCAT contrast. In the case of 20 nm Ag NPs, dimer formation induces a change in the sign of the iSCAT contrast, providing a characteristic signal for detecting binding events. 20 nm Ag NP dimers with 0.4 kDa and 3.4 kDa polyethylene glycol (PEG) spacers show iSCAT contrast distributions with significantly different averages on both wavelength channels. The iSCAT contrast measured for individual PEG-tethered 10 nm or 20 nm NP dimers as a function of time shows contrast fluctuations indicative of a rich structural dynamics in the assembled plasmonic molecules, which provides an additional metric to discern dimers from monomers and paves the path to a new class of interferometric plasmon rulers.
Collapse
Affiliation(s)
- Leslie Velasco
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Aniqa N Islam
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Koustav Kundu
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Aidan Oi
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| |
Collapse
|
30
|
Gopich IV, Chung HS. Unraveling Burst Selection Bias in Single-Molecule FRET of Species with Unequal Brightness and Diffusivity. J Phys Chem B 2024; 128:5576-5589. [PMID: 38833567 DOI: 10.1021/acs.jpcb.4c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Single-molecule free diffusion experiments enable accurate quantification of coexisting species or states. However, unequal brightness and diffusivity introduce a burst selection bias and affect the interpretation of experimental results. We address this issue with a photon-by-photon maximum likelihood method, burstML, which explicitly considers burst selection criteria. BurstML accurately estimates parameters, including photon count rates, diffusion times, Förster resonance energy transfer (FRET) efficiencies, and population, even in cases where species are poorly distinguished in FRET efficiency histograms. We develop a quantitative theory that determines the fraction of photon bursts corresponding to each species and thus obtain accurate species populations from the measured burst fractions. In addition, we provide a simple approximate formula for burst fractions and establish the range of parameters where unequal brightness and diffusivity can significantly affect the results obtained by conventional methods. The performance of the burstML method is compared with that of a maximum likelihood method that assumes equal species brightness and diffusivity, as well as standard Gaussian fitting of FRET efficiency histograms, using both simulated and real single-molecule data for cold-shock protein, protein L, and protein G. The burstML method enhances the accuracy of parameter estimation in single-molecule fluorescence studies.
Collapse
Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
31
|
Miller JJ, Mallimadugula UL, Zimmerman MI, Stuchell-Brereton MD, Soranno A, Bowman GR. Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597137. [PMID: 38895430 PMCID: PMC11185552 DOI: 10.1101/2024.06.03.597137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein's structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a protein's dynamics. This allows us to accurately assess which timescales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (Aβ40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in NMR, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings.
Collapse
Affiliation(s)
- Justin J. Miller
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Gregory R. Bowman
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| |
Collapse
|
32
|
Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
Collapse
Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
| |
Collapse
|
33
|
Renart ML, Giudici AM, González-Ros JM, Poveda JA. Steady-state and time-resolved fluorescent methodologies to characterize the conformational landscape of the selectivity filter of K + channels. Methods 2024; 225:89-99. [PMID: 38508347 DOI: 10.1016/j.ymeth.2024.02.010] [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: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
A variety of equilibrium and non-equilibrium methods have been used in a multidisciplinary approach to study the conformational landscape associated with the binding of different cations to the pore of potassium channels. These binding processes, and the conformational changes resulting therefrom, modulate the functional properties of such integral membrane properties, revealing these permeant and blocking cations as true effectors of such integral membrane proteins. KcsA, a prototypic K+ channel from Streptomyces lividans, has been extensively characterized in this regard. Here, we revise several fluorescence-based approaches to monitor cation binding under different experimental conditions in diluted samples, analyzing the advantages and disadvantages of each approach. These studies have contributed to explain the selectivity, conduction, and inactivation properties of K+ channels at the molecular level, together with the allosteric communication between the two gates that control the ion channel flux, and how they are modulated by lipids.
Collapse
Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| |
Collapse
|
34
|
Götz M, Barth A, Bohr SSR, Börner R, Chen J, Cordes T, Erie DA, Gebhardt C, Hadzic MCAS, Hamilton GL, Hatzakis NS, Hugel T, Kisley L, Lamb DC, de Lannoy C, Mahn C, Dunukara D, de Ridder D, Sanabria H, Schimpf J, Seidel CAM, Sigel RKO, Sletfjerding MB, Thomsen J, Vollmar L, Wanninger S, Weninger KR, Xu P, Schmid S. Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nat Commun 2024; 15:3626. [PMID: 38688911 PMCID: PMC11061175 DOI: 10.1038/s41467-024-47734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Markus Götz
- PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany.
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands
| | - Søren S-R Bohr
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | | | - George L Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Don C Lamb
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Carlos de Lannoy
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Chelsea Mahn
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dushani Dunukara
- Department of Physics, Case Western Reserve University, Cleveland, OH, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Julia Schimpf
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Magnus B Sletfjerding
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen, Denmark
- Novo Nordisk Center for optimised oligo escape and control of disease University of Copenhagen, 2100 Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Leonie Vollmar
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
- Department of Chemistry, University of Basel, Basel, Switzerland.
| |
Collapse
|
35
|
Gupta R, Verma SD. Two-Dimensional Fluctuation Correlation Spectroscopy (2D-FlucCS): A Method to Determine the Origin of Relaxation Rate Dispersion. ACS MEASUREMENT SCIENCE AU 2024; 4:153-162. [PMID: 38645580 PMCID: PMC11027202 DOI: 10.1021/acsmeasuresciau.3c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 04/23/2024]
Abstract
Relaxation rate dispersion, i.e., nonexponential or multicomponent kinetics, is observed in complex systems when measuring relaxation kinetics. Often, the origin of rate dispersion is associated with the heterogeneity in the system. However, both homogeneous (where all molecules experience the same rate but inherently nonexponential) and heterogeneous (where all molecules experience different rates) systems can exhibit rate dispersion. A multidimensional correlation analysis method has been demonstrated to detect and quantify rate dispersion observed in molecular rotation, diffusion, solvation, and reaction kinetics. One-dimensional (1D) autocorrelation function detects rate dispersion and measures its extent. Two-dimensional (2D) autocorrelation function measures the origin of rate dispersion and distinguishes homogeneous from heterogeneous. In a heterogeneous system, implicitly there exist subensembles of molecules experiencing different rates. A three-dimensional (3D) autocorrelation function measures subensemble exchange if present and reveals if the system possesses static or dynamic heterogeneity. This perspective discusses the principles, applications, and potential and also presents a future outlook of two-dimensional fluctuation correlation spectroscopy (2D-FlucCS). The method is applicable to any experiment or simulation where a time series of fluctuation in an observable (emission, scattering, current, etc.) around a mean value can be obtained in steady state (equilibrium or nonequilibrium), provided the system is ergodic.
Collapse
Affiliation(s)
- Ruchir Gupta
- Spectroscopy and Dynamics
Visualization Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Sachin Dev Verma
- Spectroscopy and Dynamics
Visualization Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
36
|
Roccatano D. A molecular dynamics simulation study of glycine/serine octapeptides labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene fluorophore. J Chem Phys 2024; 160:145101. [PMID: 38587229 DOI: 10.1063/5.0190073] [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: 12/03/2023] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
The compound 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is a versatile fluorophore widely used in Förster resonance energy transfer (FRET) spectroscopy studies due to its remarkable sensitivity, enabling precise donor-acceptor distance measurements, even for short peptides. Integrating time-resolved and FRET spectroscopies with molecular dynamics simulations provides a robust approach to unravel the structure and dynamics of biopolymers in a solution. This study investigates the structural behavior of three octapeptide variants: Trp-(Gly-Ser)3-Dbo, Trp-(GlyGly)3-Dbo, and Trp-(SerSer)3-Dbo, where Dbo represents the DBO-containing modified aspartic acid, using molecular dynamics simulations. Glycine- and serine-rich amino acid fragments, common in flexible protein regions, play essential roles in functional properties. Results show excellent agreement between end-to-end distances, orientational factors from simulations, and the available experimental and theoretical data, validating the reliability of the GROMOS force field model. The end-to-end distribution, modeled using three Gaussian distributions, reveals a complex shape, confirmed by cluster analysis highlighting a limited number of significant conformations dominating the peptide landscape. All peptides predominantly adopt a disordered state in the solvent, yet exhibit a compact shape, aligning with the model of disordered polypeptide chains in poor solvents. Conformations show marginal dependence on chain composition, with Ser-only chains exhibiting slightly more elongation. This study enhances our understanding of peptide behavior, providing valuable insights into their structural dynamics in solution.
Collapse
Affiliation(s)
- Danilo Roccatano
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| |
Collapse
|
37
|
Khan S, Molloy JE, Puhl H, Schulman H, Vogel SS. Real-time single-molecule imaging of CaMKII-calmodulin interactions. Biophys J 2024; 123:824-838. [PMID: 38414237 PMCID: PMC11630639 DOI: 10.1016/j.bpj.2024.02.021] [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: 08/03/2023] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy. Rhodamine-CAM associations/dissociations to surface-immobilized Venus-CaMKIIβ were resolved with 0.5 s resolution from video records, batch-processed with a custom algorithm. CAM occupancy was determined simultaneously with spot-photobleaching measurement of CaMKII holoenzyme stoichiometry. We show the ATP-dependent increase of the CAM association requires dimer formation for both the α and β isoforms. The study of mutant β holoenzymes revealed that the ATP-dependent increase in CAM affinity results in two distinct states. The phosphorylation-defective (T287.306-307A) holoenzyme resides only in the low-affinity state. CAM association is further reduced in the T287A holoenzyme relative to T287.306-307A. In the absence of ATP, the affinity of CAM for the T287.306-307A mutant and the wild-type monomer are comparable. The affinity of the ATP-binding impaired (K43R) mutant is even weaker. In ATP, the K43R holoenzyme resides in the low-affinity state. The phosphomimetic mutant (T287D) resides only in a 1000-fold higher-affinity state, with mean CAM occupancy of more than half of the 14-mer holoenzyme stoichiometry in picomolar CAM. ATP promotes T287D holoenzyme disassembly but does not elevate CAM occupancy. Single Poisson distributions characterized the ATP-dependent CAM occupancy of mutant holoenzymes. In contrast, the CAM occupancy of the wild-type population had a two-state distribution with both low- and high-affinity states represented. The low-affinity state was the dominant state, a result different from published in vitro assays. Differences in assay conditions can alter the balance between activating and inhibitory autophosphorylation. Bound ATP could be sufficient for CaMKII structural function, while antagonistic autophosphorylations may tune CaMKII kinase-regulated action-potential frequency decoding in vivo.
Collapse
Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium at Lawrence Berkeley National Laboratory, Berkeley, California.
| | | | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Howard Schulman
- Panorama Research Institute, Sunnyvale, California; Stanford University School of Medicine, Stanford, California
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| |
Collapse
|
38
|
Vallat B, Berman HM. Structural highlights of macromolecular complexes and assemblies. Curr Opin Struct Biol 2024; 85:102773. [PMID: 38271778 DOI: 10.1016/j.sbi.2023.102773] [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: 10/05/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
The structures of macromolecular assemblies have given us deep insights into cellular processes and have profoundly impacted biological research and drug discovery. We highlight the structures of macromolecular assemblies that have been modeled using integrative and computational methods and describe how open access to these structures from structural archives has empowered the research community. The arsenal of experimental and computational methods for structure determination ensures a future where whole organelles and cells can be modeled.
Collapse
Affiliation(s)
- Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles CA 90089, USA
| |
Collapse
|
39
|
Clark BS, Silvernail I, Gordon K, Castaneda JF, Morgan AN, Rolband LA, LeBlanc SJ. A practical guide to time-resolved fluorescence microscopy and spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577300. [PMID: 38586000 PMCID: PMC10996486 DOI: 10.1101/2024.01.25.577300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Förster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.
Collapse
|
40
|
Morales-Inostroza L, Folz J, Kühnemuth R, Felekyan S, Wieser FF, Seidel CAM, Götzinger S, Sandoghdar V. An optofluidic antenna for enhancing the sensitivity of single-emitter measurements. Nat Commun 2024; 15:2545. [PMID: 38514627 PMCID: PMC10957926 DOI: 10.1038/s41467-024-46730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Many single-molecule investigations are performed in fluidic environments, for example, to avoid unwanted consequences of contact with surfaces. Diffusion of molecules in this arrangement limits the observation time and the number of collected photons, thus, compromising studies of processes with fast or slow dynamics. Here, we introduce a planar optofluidic antenna (OFA), which enhances the fluorescence signal from molecules by about 5 times per passage, leads to about 7-fold more frequent returns to the observation volume, and significantly lengthens the diffusion time within one passage. We use single-molecule multi-parameter fluorescence detection (sm-MFD), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) measurements to characterize our OFAs. The antenna advantages are showcased by examining both the slow (ms) and fast (50 μs) dynamics of DNA four-way (Holliday) junctions with real-time resolution. The FRET trajectories provide evidence for the absence of an intermediate conformational state and introduce an upper bound for its lifetime. The ease of implementation and compatibility with various microscopy modalities make OFAs broadly applicable to a diverse range of studies.
Collapse
Affiliation(s)
- Luis Morales-Inostroza
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Julian Folz
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Ralf Kühnemuth
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Suren Felekyan
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Claus A M Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Stephan Götzinger
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany.
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany.
| |
Collapse
|
41
|
Bleier J, de Mendonca PRF, Habrian C, Stanley C, Vyklicky V, Isacoff EY. Conformational basis of subtype-specific allosteric control of NMDA receptor gating. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579740. [PMID: 38370786 PMCID: PMC10871359 DOI: 10.1101/2024.02.10.579740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
N-methyl-D-aspartate receptors are ionotropic glutamate receptors that are integral to synaptic transmission and plasticity. Variable GluN2 subunits in diheterotetrameric receptors with identical GluN1 subunits set very different functional properties, which support their individual physiological roles in the nervous system. To understand the conformational basis of this diversity, we assessed the conformation of the common GluN1 subunit in receptors with different GluN2 subunits using single-molecule fluorescence resonance energy transfer (smFRET). We established smFRET sensors in the ligand binding domain and modulatory amino-terminal domain to study an apo-like state and partially liganded activation intermediates, which have been elusive to structural analysis. Our results demonstrate a strong, subtype-specific influence of apo and glutamate-bound GluN2 subunits on GluN1 rearrangements, suggesting a conformational basis for the highly divergent levels of receptor activity, desensitization and agonist potency. Chimeric analysis reveals structural determinants that contribute to the subtype differences. Our study provides a framework for understanding GluN2-dependent functional properties and could open new avenues for subtype-specific modulation.
Collapse
Affiliation(s)
- Julia Bleier
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, 94720 USA
| | | | - Chris Habrian
- Department of Molecular & Cell Biology, University of California, Berkeley, California, 94720 USA
- Current address: Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Cherise Stanley
- Department of Molecular & Cell Biology, University of California, Berkeley, California, 94720 USA
| | - Vojtech Vyklicky
- Department of Molecular & Cell Biology, University of California, Berkeley, California, 94720 USA
- Current address: DIANA Biotechnologies, a.s. Průmyslová 596, 252 50 Vestec, Czech Republic
| | - Ehud Y. Isacoff
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, 94720 USA
- Department of Molecular & Cell Biology, University of California, Berkeley, California, 94720 USA
- Weill Neurohub, University of California, Berkeley, California, 94720 USA
- Molecular Biology & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| |
Collapse
|
42
|
Dasgupta S, Thomas JA, Ray K. Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches. Viruses 2024; 16:192. [PMID: 38399968 PMCID: PMC10893049 DOI: 10.3390/v16020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
Collapse
Affiliation(s)
- Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Julie A. Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA;
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| |
Collapse
|
43
|
Sano Y, Itoh Y, Kamonprasertsuk S, Suzuki L, Fukasawa A, Oikawa H, Takahashi S. Simple and Efficient Detection Scheme of Two-Color Fluorescence Correlation Spectroscopy for Protein Dynamics Investigation from Nanoseconds to Milliseconds. ACS PHYSICAL CHEMISTRY AU 2024; 4:85-93. [PMID: 38283787 PMCID: PMC10811772 DOI: 10.1021/acsphyschemau.3c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 01/30/2024]
Abstract
Nanosecond resolved fluorescence correlation spectroscopy (ns-FCS) based on two-color fluorescence detection is a powerful strategy for investigating the fast dynamics of biological macromolecules labeled with donor and acceptor fluorophores. The standard methods of ns-FCS use two single-photon avalanche diodes (SPADs) for the detection of single-color signals (four SPADs for two-color signals) to eliminate the afterpulse artifacts of SPAD at the expense of the efficiency of utilizing photon data in the calculation of correlograms. Herein, we demonstrated that hybrid photodetectors (HPDs) enable the recording of fluorescence photons in ns-FCS based on the minimal system using two HPDs for the detection of two-color signals. However, HPD exhibited afterpulses at a yield with respect to the rate of photodetection (<10-4) much lower than that of SPADs (∼10-2), which could still hamper correlation measurements. We demonstrated that the simple subtraction procedure could eliminate afterpulse artifacts. While the quantum efficiency of photodetection for HPDs is lower than that for high-performance SPADs, the developed system can be practically used for two-color ns-FCS in a time domain longer than a few nanoseconds. The fast chain dynamics of the B domain of protein A in the unfolded state was observed using the new method.
Collapse
Affiliation(s)
- Yutaka Sano
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department
of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Yuji Itoh
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department
of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate
School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Supawich Kamonprasertsuk
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department
of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Leo Suzuki
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate
School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Atsuhito Fukasawa
- Electron
Tube Division, Hamamatsu Photonics K. K., Iwata, Shizuoka 438-0193, Japan
| | - Hiroyuki Oikawa
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department
of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate
School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- MOLCURE, Kawasaki, Kanagawa 212-0032, Japan
| | - Satoshi Takahashi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department
of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate
School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| |
Collapse
|
44
|
Verma AR, Ray KK, Bodick M, Kinz-Thompson CD, Gonzalez RL. Increasing the accuracy of single-molecule data analysis using tMAVEN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.15.553409. [PMID: 37645812 PMCID: PMC10462008 DOI: 10.1101/2023.08.15.553409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Time-dependent single-molecule experiments contain rich kinetic information about the functional dynamics of biomolecules. A key step in extracting this information is the application of kinetic models, such as hidden Markov models (HMMs), which characterize the molecular mechanism governing the experimental system. Unfortunately, researchers rarely know the physico-chemical details of this molecular mechanism a priori, which raises questions about how to select the most appropriate kinetic model for a given single-molecule dataset and what consequences arise if the wrong model is chosen. To address these questions, we have developed and used time-series Modeling, Analysis, and Visualization ENvironment (tMAVEN), a comprehensive, open-source, and extensible software platform. tMAVEN can perform each step of the single-molecule analysis pipeline, from pre-processing to kinetic modeling to plotting, and has been designed to enable the analysis of a single-molecule dataset with multiple types of kinetic models. Using tMAVEN, we have systematically investigated mismatches between kinetic models and molecular mechanisms by analyzing simulated examples of prototypical single-molecule datasets exhibiting common experimental complications, such as molecular heterogeneity, with a series of different types of HMMs. Our results show that no single kinetic modeling strategy is mathematically appropriate for all experimental contexts. Indeed, HMMs only correctly capture the underlying molecular mechanism in the simplest of cases. As such, researchers must modify HMMs using physico-chemical principles to avoid the risk of missing the significant biological and biophysical insights into molecular heterogeneity that their experiments provide. By enabling the facile, side-by-side application of multiple types of kinetic models to individual single-molecule datasets, tMAVEN allows researchers to carefully tailor their modeling approach to match the complexity of the underlying biomolecular dynamics and increase the accuracy of their single-molecule data analyses.
Collapse
Affiliation(s)
- Anjali R. Verma
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | - Korak Kumar Ray
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | - Maya Bodick
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| | | | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027 USA
| |
Collapse
|
45
|
Vermeer B, van Ossenbruggen J, Schmid S. Single-Molecule FRET-Resolved Protein Dynamics - from Plasmid to Data in Six Steps. Methods Mol Biol 2024; 2694:267-291. [PMID: 37824009 DOI: 10.1007/978-1-0716-3377-9_13] [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] [Indexed: 10/13/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for the detection of conformational dynamics of biomolecules. While many smFRET experiments are performed using dye-labeled DNA, here we describe a comprehensive protocol to resolve the conformational dynamics of a protein system - notably from plasmid to data. Using the example of the heat-shock protein Hsp90, we describe the protein production and threefold site-specific bioconjugation, the smFRET measurement using total internal reflection fluorescence microscopy (TIRFM), and raw data processing to reveal time-resolved protein dynamics. The described smFRET approach is readily transferrable to the study of many more all-protein systems and their conformational energy landscape.
Collapse
Affiliation(s)
- Benjamin Vermeer
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Sonja Schmid
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.
| |
Collapse
|
46
|
Filius M, van Wee R, Joo C. Single-Molecule FRET X. Methods Mol Biol 2024; 2694:203-213. [PMID: 37824006 DOI: 10.1007/978-1-0716-3377-9_10] [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] [Indexed: 10/13/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short fluorescently labeled DNA imager strands specifically and transiently bind their complementary docking strands on a target molecule, such that at most a single FRET pair is formed at each point in time and multiple POIs on a single molecule can be readily probed. Here, we describe the sample preparation, image acquisition, and data analysis for structural analysis of DNA nanostructures with FRET X.
Collapse
Affiliation(s)
- Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
| |
Collapse
|
47
|
Coutinho A, Poveda JA, Renart ML. Conformational Dynamic Studies of Prokaryotic Potassium Channels Explored by Homo-FRET Methodologies. Methods Mol Biol 2024; 2796:35-72. [PMID: 38856894 DOI: 10.1007/978-1-0716-3818-7_3] [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] [Indexed: 06/11/2024]
Abstract
Fluorescence techniques have been widely used to shed light over the structure-function relationship of potassium channels for the last 40-50 years. In this chapter, we describe how a Förster resonance energy transfer between identical fluorophores (homo-FRET) approach can be applied to study the gating behavior of the prokaryotic channel KcsA. Two different gates have been described to control the K+ flux across the channel's pore, the helix-bundle crossing and the selectivity filter, located at the opposite sides of the channel transmembrane section. Both gates can be studied individually or by using a double-reporter system. Due to its homotetrameric structural arrangement, KcsA presents a high degree of symmetry that fulfills the first requisite to calculate intersubunit distances through this technique. The results obtained through this work have helped to uncover the conformational plasticity of the selectivity filter under different experimental conditions and the importance of its allosteric coupling to the opening of the activation (inner) gate. This biophysical approach usually requires low protein concentration and presents high sensitivity and reproducibility, complementing the high-resolution structural information provided by X-ray crystallography, cryo-EM, and NMR studies.
Collapse
Affiliation(s)
- Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain
| | - María Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain.
| |
Collapse
|
48
|
Shrestha P, Yang D, Ward A, Shih WM, Wong WP. Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers. J Am Chem Soc 2023; 145:27916-27921. [PMID: 38096567 PMCID: PMC10755700 DOI: 10.1021/jacs.3c10262] [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: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023]
Abstract
The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement with previously reported structures.
Collapse
Affiliation(s)
- Prakash Shrestha
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darren Yang
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Ward
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
| | - William M. Shih
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wesley P. Wong
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
49
|
Heubach CA, Hasanbasri Z, Abdullin D, Reuter A, Korzekwa B, Saxena S, Schiemann O. Differentiating between Label and Protein Conformers in Pulsed Dipolar EPR Spectroscopy with the dHis-Cu 2+ (NTA) Motif. Chemistry 2023; 29:e202302541. [PMID: 37755452 DOI: 10.1002/chem.202302541] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
Pulsed dipolar EPR spectroscopy (PDS) in combination with site-directed spin labeling is a powerful tool in structural biology. However, the commonly used spin labels are conjugated to biomolecules via rather long and flexible linkers, which hampers the translation of distance distributions into biomolecular conformations. In contrast, the spin label copper(II)-nitrilotriacetic acid [Cu2+ (NTA)] bound to two histidines (dHis) is rigid and yields narrow distance distributions, which can be more easily translated into biomolecular conformations. Here, we use this label on the 71 kDa Yersinia outer protein O (YopO) to decipher whether a previously experimentally observed bimodal distance distribution is due to two conformations of the biomolecule or of the flexible spin labels. Two different PDS experiments, that is, pulsed electron-electron double resonance (PELDOR aka DEER) and relaxation-induced dipolar modulation enhancement (RIDME), yield unimodal distance distribution with the dHis-Cu2+ (NTA) motif; this result suggests that the α-helical backbone of YopO adopts a single conformation in frozen solution. In addition, we show that the Cu2+ (NTA) label preferentially binds to the target double histidine (dHis) sites even in the presence of 22 competing native histidine residues. Our results therefore suggest that the generation of a His-null background is not required for this spin labeling methodology. Together these results highlight the value of the dHis-Cu2+ (NTA) motif in PDS experiments.
Collapse
Affiliation(s)
- Caspar A Heubach
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Zikri Hasanbasri
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Arne Reuter
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Benedict Korzekwa
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
- Leibniz-Center for Diabetes Research, University of Düsseldorf, Auf'm Hennekamp 65, 40225, Düsseldorf, Germany
| | - Sunil Saxena
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| |
Collapse
|
50
|
Luginina A, Maslov I, Khorn P, Volkov O, Khnykin A, Kuzmichev P, Shevtsov M, Belousov A, Kapranov I, Dashevskii D, Kornilov D, Bestsennaia E, Hofkens J, Hendrix J, Gensch T, Cherezov V, Ivanovich V, Mishin A, Borshchevskiy V. Functional GPCR Expression in Eukaryotic LEXSY System. J Mol Biol 2023; 435:168310. [PMID: 37806553 DOI: 10.1016/j.jmb.2023.168310] [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: 06/29/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
G protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins in the human genome, and represent one of the most important classes of drug targets. Their structural studies facilitate rational drug discovery. However, atomic structures of only about 20% of human GPCRs have been solved to date. Recombinant production of GPCRs for structural studies at a large scale is challenging due to their low expression levels and stability. Therefore, in this study, we explored the efficacy of the eukaryotic system LEXSY (Leishmania tarentolae) for GPCR production. We selected the human A2A adenosine receptor (A2AAR), as a model protein, expressed it in LEXSY, purified it, and compared with the same receptor produced in insect cells, which is the most popular expression system for structural studies of GPCRs. The A2AAR purified from both expression systems showed similar purity, stability, ligand-induced conformational changes and structural dynamics, with a remarkably higher protein yield in the case of LEXSY expression. Overall, our results suggest that LEXSY is a promising platform for large-scale production of GPCRs for structural studies.
Collapse
Affiliation(s)
- Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | | | - Andrey Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Anatoliy Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dmitrii Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Daniil Kornilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ekaterina Bestsennaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium; Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Joint Institute for Nuclear Research, Dubna, Russia.
| |
Collapse
|