1
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Zenker S, Lohmann J, Chiorescu I, Krüger S, Kumke MU, Reich T, Schmeide K, Kretzschmar J. Complexation of Ln(III) Ions by Gluconate: Joint Investigation Applying TRLFS, CE-ICP-MS, NMR, and DF Calculations. Inorg Chem 2025; 64:7970-7987. [PMID: 40214153 PMCID: PMC12042262 DOI: 10.1021/acs.inorgchem.4c05476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/14/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025]
Abstract
The potential of gluconate, a common cement additive, to mobilize lanthanides (used as analogues of actinides) from cement is investigated. For this purpose, complex formation of trivalent lanthanides, Ln(III), (Ln: La, Sm, Eu, Gd, Lu) with gluconate (GLU) was studied applying time-resolved laser-induced luminescence spectroscopy (TRLFS) in combination with parallel factor analysis (PARAFAC), capillary electrophoresis-inductively coupled plasma mass spectrometry (CE-ICP-MS), nuclear magnetic resonance (NMR) spectroscopy, and density functional (DF) calculations. Up to circumneutral conditions, binary complexes form with Ln(III):GLU stoichiometric ratios of 1:1-1:4 depending only on the Ln:GLU ratio, regardless of the concentration regime (micromolar to millimolar). Coordination facilitates via the carboxyl group (C1) and the adjacent hydroxyl group (at C2) forming a five-membered ring chelation motif, with a probable participation of the C3 hydroxyl group. Beyond circumneutral pH, with the exact onset depending on the specific lanthanide, a fundamental change in speciation takes place. Speciation then becomes more complex upon coexistence and interconversion of several (isomeric) complexes concluded to involve one or more deprotonated GLU hydroxyl groups not necessarily participating in coordination.
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Affiliation(s)
- Sophie Zenker
- Institute
of Chemistry, Universität Potsdam, Potsdam 14476, Germany
| | - Janik Lohmann
- Department
of Chemistry, Johannes Gutenberg-Universität
Mainz, Mainz 55128, Germany
| | - Ion Chiorescu
- Chemistry
Department, School of Natural Sciences, Technische Universität München, Garching 85748, Germany
| | - Sven Krüger
- Chemistry
Department, School of Natural Sciences, Technische Universität München, Garching 85748, Germany
| | - Michael U. Kumke
- Institute
of Chemistry, Universität Potsdam, Potsdam 14476, Germany
| | - Tobias Reich
- Department
of Chemistry, Johannes Gutenberg-Universität
Mainz, Mainz 55128, Germany
| | - Katja Schmeide
- Institute
of Resource Ecology, Helmholtz-Zentrum Dresden–Rossendorf, Dresden 01328, Germany
| | - Jerome Kretzschmar
- Institute
of Resource Ecology, Helmholtz-Zentrum Dresden–Rossendorf, Dresden 01328, Germany
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2
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Dhiman M, Escobar L, Smith JT, Hunter CA. Cooperativity in the assembly of H-bonded duplexes of synthetic recognition-encoded melamine oligomers. Chem Sci 2025; 16:5995-6002. [PMID: 40060096 PMCID: PMC11886990 DOI: 10.1039/d4sc08591d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 03/02/2025] [Indexed: 04/04/2025] Open
Abstract
Recognition-encoded melamine oligomers (REMO) are synthetic polymers composed of repeating triazine-piperazine units and equipped with phenol and phosphine oxide side-chains. Short oligomers have previously been shown to form length- and sequence-selective H-bonded duplexes in non-polar solvents. Here, automated solid phase synthesis was used to prepare homo-sequence REMO with either twelve phenol recognition units or twelve phosphine oxide recognition units. The ends of the oligomers were functionalised with an azide and an alkyne group to allow investigation of duplex formation by covalent trapping with copper-catalysed azide-alkyne cycloaddition (CuAAC) reactions. The oligomers were also functionalised with a dansyl fluorophore or a dabcyl quencher dye to allow investigation of duplex formation by Förster resonance energy transfer (FRET). Covalent trapping showed that the duplex is the major species present in a 1 : 1 mixture of the phenol 12-mer and phosphine oxide 12-mer at micromolar concentrations in dichloromethane. FRET titration experiments showed that the association constant for duplex formation is greater than 108 M-1 in chloroform, and DMSO denaturation experiments showed that duplex formation is highly cooperative. The Hill coefficient for denaturation of the 12-mer duplex was 4.6, which is significantly higher than the value measured for the corresponding 6-mer duplex (1.9). This behaviour mirrors that observed for nucleic acid duplexes, where denaturation becomes increasingly cooperative as more base-pairs are added to the duplex.
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Affiliation(s)
- Mohit Dhiman
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Luis Escobar
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Joseph T Smith
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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3
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Girvan P, Ying L, Dodson CA. Tetramethylrhodamine self-quenching is a probe of conformational change on the scale of 15-25 Å. Chem Commun (Camb) 2025; 61:5353-5356. [PMID: 40084975 PMCID: PMC11908412 DOI: 10.1039/d4cc04524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 02/27/2025] [Indexed: 03/16/2025]
Abstract
Tetramethylrhodamine (TMR) is a fluorescent dye whose self-quenching has been used as a probe of multiple biological phenomena. We determine the distance-dependence of self-quenching and place bounds on the timescale of TMR dissociation. Our results validate fluorescence self-quenching as an alternative to FRET and enable future assays to be designed with confidence.
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Affiliation(s)
- Paul Girvan
- Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, London SW7 2AZ, UK.
| | - Liming Ying
- National Heart & Lung Institute, Imperial College London, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12 0BZ, UK
| | - Charlotte A Dodson
- Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, London SW7 2AZ, UK.
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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4
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Nüesch M, Ivanović MT, Nettels D, Best RB, Schuler B. Accuracy of distance distributions and dynamics from single-molecule FRET. Biophys J 2025:S0006-3495(25)00202-4. [PMID: 40165371 DOI: 10.1016/j.bpj.2025.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 02/12/2025] [Accepted: 03/26/2025] [Indexed: 04/02/2025] Open
Abstract
Single-molecule spectroscopy combined with Förster resonance energy transfer is widely used to quantify distance dynamics and distributions in biomolecules. Most commonly, measurements are interpreted using simple analytical relations between experimental observables and the underlying distance distributions. However, these relations make simplifying assumptions, such as a separation of timescales between interdye distance dynamics, fluorescence lifetimes, and dye reorientation, the validity of which is notoriously difficult to assess from experimental data alone. Here, we use experimentally validated long-timescale, all-atom explicit-solvent molecular dynamics simulations of a disordered peptide with explicit fluorophores for testing these assumptions, in particular the separation of the relevant timescales and the description of chain dynamics in terms of diffusion in a potential of mean force. Our results allow us to quantitatively assess the resulting errors; they indicate that, even outside the simple limiting regimes, the errors from common approximations in data analysis are generally smaller than the systematic uncertainty limiting the accuracy of Förster resonance energy transfer efficiencies. We also illustrate how the direct comparison between measured and simulated experimental data can be employed to optimize force field parameters and develop increasingly realistic simulation models.
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Affiliation(s)
- Mark Nüesch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Miloš T Ivanović
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Physics, University of Zurich, Zurich, Switzerland.
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5
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Gonzalo D, Cupellini L, Curutchet C. On the breakdown of Förster energy transfer theory due to solvent effects: atomistic simulations unveil distance-dependent dielectric screening in calmodulin. Chem Sci 2025; 16:3693-3704. [PMID: 39886442 PMCID: PMC11775579 DOI: 10.1039/d4sc07679f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 01/21/2025] [Indexed: 02/01/2025] Open
Abstract
Förster resonance energy transfer (FRET) is a powerful technique used to investigate the conformational preferences of biosystems, and molecular simulations have emerged as an ideal complement to FRET due to their ability to provide structural models that can be compared with experiments. This synergy is however hampered by the approximations underlying Förster theory regarding the electronic coupling between the participating dyes: a dipole-dipole term attenuated by a simple dielectric screening factor 1/n 2 that depends on the refractive index of the medium. Whereas the limits of the dipole approximation are well-known, detailed insights on how environment effects deviate from the 1/n 2 assumption and modify the R -6 distance dependence that characterizes FRET as a spectroscopic ruler are still not well understood, especially in biosystems characterized by significant structural disorder. Here we address this using a rigorous theoretical framework based on electrostatic potential-fitted transition charges coupled to an atomistic polarizable classical environment, which allows investigation of dielectric screening in atomic detail in extended simulations of disordered systems. We apply this strategy to investigate the conformational preferences of calmodulin, a protein that plays a major role in the transmission of calcium signals. Our results indicate that dielectric screening displays an exponential decay at donor/acceptor separations below 20 Å, significantly modifying the R -6 distance dependence widely adopted in FRET studies. Screening appears to be maximized at separations ∼15 Å, a situation in which the fluorophores are partially excluded from the solvent and thus screening is dictated by the more polarizable protein environment.
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Affiliation(s)
- Daniel Gonzalo
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB) Barcelona Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB) Barcelona Spain
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa 56126 Pisa Italy
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB) Barcelona Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB) Barcelona Spain
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6
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Peulen TO, Hemmen K, Greife A, Webb BM, Felekyan S, Sali A, Seidel CAM, Sanabria H, Heinze KG. tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. Bioinformatics 2025; 41:btaf025. [PMID: 39836627 PMCID: PMC11796090 DOI: 10.1093/bioinformatics/btaf025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 01/04/2025] [Accepted: 01/17/2025] [Indexed: 01/23/2025] Open
Abstract
SUMMARY We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines to unify various spectroscopic analysis tools. Our software can be used for processing multiple experiment types, e.g. for time-resolved single-molecule spectroscopy, laser scanning microscopy, fluorescence correlation spectroscopy and image correlation spectroscopy. The software is file format agnostic and processes multiple time-resolved data formats and outputs. Our software eliminates the need for data conversion and mitigates data archiving issues. AVAILABILITY AND IMPLEMENTATION tttrlib is available via pip (https://pypi.org/project/tttrlib/) and bioconda while the open-source code is available via GitHub (https://github.com/fluorescence-tools/tttrlib). Presented examples and additional documentation demonstrating how to implement in vitro and live-cell image spectroscopy analysis are available at https://docs.peulen.xyz/tttrlib and https://zenodo.org/records/14002224.
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Affiliation(s)
- Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and Quantitative Biosciences Institute, University of California, San Francisco, CA, 94143, United States
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg (JMU), Würzburg, 97080, Germany
| | - Katherina Hemmen
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg (JMU), Würzburg, 97080, Germany
| | - Annemarie Greife
- Chair of Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, 40225, Germany
| | - Benjamin M Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and Quantitative Biosciences Institute, University of California, San Francisco, CA, 94143, United States
| | - Suren Felekyan
- Chair of Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, 40225, Germany
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and Quantitative Biosciences Institute, University of California, San Francisco, CA, 94143, United States
| | - Claus A M Seidel
- Chair of Molecular Physical Chemistry, Heinrich-Heine University, Düsseldorf, 40225, Germany
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC, 29634, United States
| | - Katrin G Heinze
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg (JMU), Würzburg, 97080, Germany
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7
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Lam AYW, Tsuboyama K, Tadakuma H, Tomari Y. DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43. RNA (NEW YORK, N.Y.) 2024; 30:1422-1436. [PMID: 39117455 PMCID: PMC11482610 DOI: 10.1261/rna.080165.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024]
Abstract
Many RNA-binding proteins (RBPs) contain low-complexity domains (LCDs) with prion-like compositions. These long intrinsically disordered regions regulate their solubility, contributing to their physiological roles in RNA processing and organization. However, this also makes these RBPs prone to pathological misfolding and aggregation that are characteristic of neurodegenerative diseases. For example, TAR DNA-binding protein 43 (TDP-43) forms pathological aggregates associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While molecular chaperones are well-known suppressors of these aberrant events, we recently reported that highly disordered, hydrophilic, and charged heat-resistant obscure (Hero) proteins may have similar effects. Specifically, Hero proteins can maintain the activity of other proteins from denaturing conditions in vitro, while their overexpression can suppress cellular aggregation and toxicity associated with aggregation-prone proteins. However, it is unclear how these protective effects are achieved. Here, we used single-molecule FRET to monitor the conformations of the aggregation-prone prion-like LCD of TDP-43. While we observed high conformational heterogeneity in wild-type LCD, the ALS-associated mutation A315T promoted collapsed conformations. In contrast, an Hsp40 chaperone, DNAJA2, and a Hero protein, Hero11, stabilized extended states of the LCD, consistent with their ability to suppress the aggregation of TDP-43. Our results link single-molecule effects on conformation to macro effects on bulk aggregation, where a Hero protein, like a chaperone, can maintain the conformational integrity of a client protein to prevent its aggregation.
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Affiliation(s)
- Andy Y W Lam
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kotaro Tsuboyama
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Institute of Industrial Science, the University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Hisashi Tadakuma
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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8
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Sahl SJ, Matthias J, Inamdar K, Weber M, Khan TA, Brüser C, Jakobs S, Becker S, Griesinger C, Broichhagen J, Hell SW. Direct optical measurement of intramolecular distances with angstrom precision. Science 2024; 386:180-187. [PMID: 39388556 DOI: 10.1126/science.adj7368] [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: 07/13/2023] [Accepted: 09/03/2024] [Indexed: 10/12/2024]
Abstract
Optical investigations of nanometer distances between proteins, their subunits, or other biomolecules have been the exclusive prerogative of Förster resonance energy transfer (FRET) microscopy for decades. In this work, we show that MINFLUX fluorescence nanoscopy measures intramolecular distances down to 1 nanometer-and in planar projections down to 1 angstrom-directly, linearly, and with angstrom precision. Our method was validated by quantifying well-characterized 1- to 10-nanometer distances in polypeptides and proteins. Moreover, we visualized the orientations of immunoglobulin subunits, applied the method in human cells, and revealed specific configurations of a histidine kinase PAS domain dimer. Our results open the door for examining proximities and interactions by direct position measurements at the intramacromolecular scale.
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Affiliation(s)
- Steffen J Sahl
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Jessica Matthias
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Kaushik Inamdar
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Michael Weber
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Taukeer A Khan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Christian Brüser
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy TNM, Göttingen 37075, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen 37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy TNM, Göttingen 37075, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Christian Griesinger
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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9
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Venturelli A, Guaitoli G, Vanossi D, Saitta F, Fessas D, Vitiello S, Malpezzi G, Aiello D, Ferrari S, Tondi D, Ponterini G, Paola Costi M. Intersite communication in dimeric enzymes highlighted by structural and thermodynamic analysis of didansyltyrosine binding to thymidylate synthases. Bioorg Chem 2024; 151:107663. [PMID: 39088977 DOI: 10.1016/j.bioorg.2024.107663] [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: 06/01/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/03/2024]
Abstract
Intersite communication in dimeric enzymes, triggered by ligand binding, represents both a challenge and an opportunity in enzyme inhibition strategy. Though often understestimated, it can impact on the in vivo biological mechansim of an inhibitor and on its pharmacokinetics. Thymidylate synthase (TS) is a homodimeric enzyme present in almost all living organisms that plays a crucial role in DNA synthesis and cell replication. While its inhibition is a valid strategy in the therapy of several human cancers, designing specific inhibitors of bacterial TSs poses a challenge to the development of new anti-infective agents. N,O-didansyl-l-tyrosine (DDT) inhibits both Escherichia coli TS (EcTS) and Lactobacillus casei TS (LcTS). The available X-ray structure of the DDT:dUMP:EcTS ternary complex indicated an unexpected binding mode for DDT to EcTS, involving a rearrangement of the protein and addressing the matter of communication between the two active sites of an enzyme dimer. Combining molecular-level information on DDT binding to EcTS and LcTS extracted from structural and FRET-based fluorometric evidence with a thermodynamic characterization of these events obtained by fluorometric and calorimetric titrations, this study unveiled a negative cooperativity between the DDT bindings to the two monomers of each enzyme dimer. This result, complemented by the species-specific thermodynamic signatures of the binding events, implied that communication across the protein dimer was triggered by the first DDT binding. These findings could challenge the conventional understanding of TS inhibition and open the way for the development of novel TS inhibitors with a different mechanism of action and enhanced efficacy and specificity.
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Affiliation(s)
- Alberto Venturelli
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giambattista Guaitoli
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; Evotec SE, Biophysic - Essener Bogen 7, 22419 Hamburg, Germany
| | - Davide Vanossi
- Dipartimento di Scienze Chimiche e Geologiche, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Francesca Saitta
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Dimitrios Fessas
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Simone Vitiello
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulia Malpezzi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; Clinical and Experimental Medicine (CEM) PhD Program, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Daniele Aiello
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefania Ferrari
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Donatella Tondi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Glauco Ponterini
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Maria Paola Costi
- Dipartimento di Scienze della Vita, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
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10
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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.
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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.
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11
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Jacobi R, González L. Resonance energy transfer in orthogonally arranged chromophores: a question of molecular representation. Phys Chem Chem Phys 2024; 26:12299-12305. [PMID: 38602332 DOI: 10.1039/d4cp00420e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Energy transfer between orthogonally arranged chromophores is typically considered impossible according to conventional Förster resonance energy transfer theory. Nevertheless, the disruption of orthogonality by nuclear vibrations can enable energy transfer, what has prompted the necessity for formal expansions of the standard theory. Here, we propose that there is no need to extend conventional Förster theory in such cases. Instead, a more accurate representation of the chromophores is required. Through calculations of the energy transfer rate using structures from a thermal ensemble, rather than relying on equilibrium geometries, we show that the standard Förster resonance energy transfer theory is still capable of describing energy transfer in orthogonally arranged systems. Our calculations explain how thermal vibrations influence the electronic properties of the states involved in energy transfer, affecting the alignment of transition dipole moments and the intensity of transitions.
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Affiliation(s)
- Richard Jacobi
- Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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12
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Pietrek LM, Stelzl LS, Hummer G. Hierarchical Assembly of Single-Stranded RNA. J Chem Theory Comput 2024; 20:2246-2260. [PMID: 38361440 PMCID: PMC10938505 DOI: 10.1021/acs.jctc.3c01049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/09/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024]
Abstract
Single-stranded RNA (ssRNA) plays a major role in the flow of genetic information-most notably, in the form of messenger RNA (mRNA)-and in the regulation of biological processes. The highly dynamic nature of chains of unpaired nucleobases challenges structural characterizations of ssRNA by experiments or molecular dynamics (MD) simulations alike. Here, we use hierarchical chain growth (HCG) to construct ensembles of ssRNA chains. HCG assembles the structures of protein and nucleic acid chains from fragment libraries created by MD simulations. Applied to homo- and heteropolymeric ssRNAs of different lengths, we find that HCG produces structural ensembles that overall are in good agreement with diverse experiments, including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET). The agreement can be further improved by ensemble refinement using Bayesian inference of ensembles (BioEn). HCG can also be used to assemble RNA structures that combine base-paired and base-unpaired regions, as illustrated for the 5' untranslated region (UTR) of SARS-CoV-2 RNA.
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Affiliation(s)
- Lisa M. Pietrek
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Lukas S. Stelzl
- Faculty
of Biology, Johannes Gutenberg University
Mainz, Gresemundweg 2, 55128 Mainz, Germany
- KOMET
1, Institute of Physics, Johannes Gutenberg
University Mainz, 55099 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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13
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Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries. Commun Biol 2024; 7:298. [PMID: 38461354 PMCID: PMC10925062 DOI: 10.1038/s42003-024-05910-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024] Open
Abstract
Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict .
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Affiliation(s)
- Daniele Montepietra
- Department of Chemical, Life and Environmental Sustainability Sciences, University of Parma, Parma, 43125, Italy
- Istituto Nanoscienze - CNR-NANO, Center S3, via G. Campi 213/A, 41125, Modena, Italy
| | - Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - João M Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.
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14
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Waly SMA, Benniston AC, Harriman A. Deducing the conformational space for an octa-proline helix. Chem Sci 2024; 15:1657-1671. [PMID: 38303943 PMCID: PMC10829019 DOI: 10.1039/d3sc05287g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.
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Affiliation(s)
- Sara M A Waly
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Andrew C Benniston
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
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15
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Tsai CL, Chang JW, Cheng KY, Lan YJ, Hsu YC, Lin QD, Chen TY, Shih O, Lin CH, Chiang PH, Simenas M, Kalendra V, Chiang YW, Chen CH, Jeng US, Wang SK. Comprehensive characterization of polyproline tri-helix macrocyclic nanoscaffolds for predictive ligand positioning. NANOSCALE ADVANCES 2024; 6:947-959. [PMID: 38298598 PMCID: PMC10825903 DOI: 10.1039/d3na00945a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Multivalent ligands hold promise for enhancing avidity and selectivity to simultaneously target multimeric proteins, as well as potentially modulating receptor signaling in pharmaceutical applications. Essential for these manipulations are nanosized scaffolds that precisely control ligand display patterns, which can be achieved by using polyproline oligo-helix macrocyclic nanoscaffolds via selective binding to protein oligomers and cell surface receptors. This work focuses on synthesis and structural characterization of different-sized polyproline tri-helix macrocyclic (PP3M) scaffolds. Through combined analysis of circular dichroism (CD), small- and wide-angle X-ray scattering (SWAXS), electron spin resonance (ESR) spectroscopy, and molecular modeling, a non-coplanar tri-helix loop structure with partially crossover helix ends is elucidated. This structural model aligns well with scanning tunneling microscopy (STM) imaging. The present work enhances the precision of nanoscale organic synthesis, offering prospects for controlled ligand positioning on scaffolds. This advancement paves the way for further applications in nanomedicine through selective protein interaction, manipulation of cell surface receptor functions, and developments of more complex polyproline-based nanostructures.
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Affiliation(s)
- Chia-Lung Tsai
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Kum-Yi Cheng
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Yi-Cheng Hsu
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Qun-Da Lin
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Tzu-Yuan Chen
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Chih-Hsun Lin
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Po-Hsun Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Mantas Simenas
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Vidmantas Kalendra
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Chun-Hsien Chen
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
- Department of Chemical Engineering, National Tsing Hua University Hsinchu 300044 Taiwan
- College of Semiconductor Research, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University Hsinchu 300044 Taiwan
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16
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Oltrogge LM, Chen AW, Chaijarasphong T, Turnšek JB, Savage DF. α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry 2024; 63:219-229. [PMID: 38085650 PMCID: PMC10795168 DOI: 10.1021/acs.biochem.3c00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constituent proteins into an icosahedral shell, which encapsulates the enzymes Rubisco and carbonic anhydrase to form structures typically > 100 nm and > 300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here, we show that the size of α-carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats that bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of α-carboxysomes.
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Affiliation(s)
- Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Allen W. Chen
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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17
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Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 2023; 83:102726. [PMID: 37924569 DOI: 10.1016/j.sbi.2023.102726] [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: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
Abstract
Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review, we summarize present knowledge for the most abundant homorepeats, highlighting the role of the inherent structure and the conformational influence exerted by their flanking regions. Recent experimental and computational methods enable residue-specific investigations of these regions and promise novel structural and dynamic information for this elusive group of proteins. This information should increase our knowledge about the structural bases of phenomena such as liquid-liquid phase separation and trinucleotide repeat disorders.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France. https://twitter.com/carloselenareal
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France.
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18
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Wu X, Barner-Kowollik C. Fluorescence-readout as a powerful macromolecular characterisation tool. Chem Sci 2023; 14:12815-12849. [PMID: 38023522 PMCID: PMC10664555 DOI: 10.1039/d3sc04052f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The last few decades have witnessed significant progress in synthetic macromolecular chemistry, which can provide access to diverse macromolecules with varying structural complexities, topology and functionalities, bringing us closer to the aim of controlling soft matter material properties with molecular precision. To reach this goal, the development of advanced analytical techniques, allowing for micro-, molecular level and real-time investigation, is essential. Due to their appealing features, including high sensitivity, large contrast, fast and real-time response, as well as non-invasive characteristics, fluorescence-based techniques have emerged as a powerful tool for macromolecular characterisation to provide detailed information and give new and deep insights beyond those offered by commonly applied analytical methods. Herein, we critically examine how fluorescence phenomena, principles and techniques can be effectively exploited to characterise macromolecules and soft matter materials and to further unravel their constitution, by highlighting representative examples of recent advances across major areas of polymer and materials science, ranging from polymer molecular weight and conversion, architecture, conformation to polymer self-assembly to surfaces, gels and 3D printing. Finally, we discuss the opportunities for fluorescence-readout to further advance the development of macromolecules, leading to the design of polymers and soft matter materials with pre-determined and adaptable properties.
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Affiliation(s)
- Xingyu Wu
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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19
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Nepal S, Holmstrom ED. Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein. J Virol 2023; 97:e0089223. [PMID: 37772835 PMCID: PMC10617558 DOI: 10.1128/jvi.00892-23] [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: 06/14/2023] [Accepted: 08/10/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The hepatitis C virus is associated with nearly 300,000 deaths annually. At the core of the virus is an RNA-protein complex called the nucleocapsid, which consists of the viral genome and many copies of the core protein. Because the assembly of the nucleocapsid is a critical step in viral replication, a considerable amount of effort has been devoted to identifying antiviral therapeutics that can bind to the core protein and disrupt assembly. Although several candidates have been identified, little is known about how they interact with the core protein or how those interactions alter the structure and thus the function of this viral protein. Our work biochemically characterizes several of these binding interactions, highlighting both similarities and differences as well as strengths and weaknesses. These insights bolster the notion that this viral protein is a viable target for novel therapeutics and will help to guide future developments of these candidate antivirals.
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Affiliation(s)
- Sudip Nepal
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Erik D. Holmstrom
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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20
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Detwiler R, McPartlon TJ, Coffey CS, Kramer JR. Clickable Polyprolines from Azido-proline N-Carboxyanhydride. ACS POLYMERS AU 2023; 3:383-393. [PMID: 37841952 PMCID: PMC10571246 DOI: 10.1021/acspolymersau.3c00011] [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: 05/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 10/17/2023]
Abstract
Polyproline is a material of great interest in biomedicine due to its helical scaffold of structural importance in collagen and mucins and its ability to gel and to change conformations in response to temperature. Appending of function-modulating chemical groups to such a material is desirable to diversify potential applications. Here, we describe the synthesis of high-molecular-weight homo, block, and statistical polymers of azide-functionalized proline. The azide groups served as moieties for highly efficient click-grafting, as stabilizers of the polyproline PPII helix, and as modulators of thermoresponsiveness. Saccharides and ethylene glycol were utilized to explore small-molecule grafting, and glutamate polymers were utilized to form polyelectrolyte bottlebrush architectures. Secondary structure effects of both the azide and click modifications, as well as lower critical solution temperature behavior, were characterized. The polyazidoprolines and click products were well tolerated by live human cells and are expected to find use in diverse biomedical applications.
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Affiliation(s)
- Rachel
E. Detwiler
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
| | - Thomas J. McPartlon
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
| | - Clara S. Coffey
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
| | - Jessica R. Kramer
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
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21
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Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J. Robust and scalable single-molecule protein sequencing with fluorosequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558007. [PMID: 37745461 PMCID: PMC10516020 DOI: 10.1101/2023.09.15.558007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.
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Affiliation(s)
| | | | - Heather D Stout
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | - Christopher Martin
- Erisyon, Inc. Austin, TX, 78752
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | | | - Fan Tu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | | | | | | | | | | | | | - Angela M Bardo
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jagannath Swaminathan
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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22
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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23
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Heesink G, Marseille MJ, Fakhree MAA, Driver MD, van Leijenhorst-Groener KA, Onck PR, Blum C, Claessens MM. Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations. Biomacromolecules 2023; 24:3680-3688. [PMID: 37407505 PMCID: PMC10428166 DOI: 10.1021/acs.biomac.3c00404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Theoretical concepts from polymer physics are often used to describe intrinsically disordered proteins (IDPs). However, amino acid interactions within and between regions of the protein can lead to deviations from typical polymer scaling behavior and even to short-lived secondary structures. To investigate the key interactions in the dynamic IDP α-synuclein (αS) at the amino acid level, we conducted single-molecule fluorescence resonance energy transfer (smFRET) experiments and coarse-grained molecular dynamics (CG-MD) simulations. We find excellent agreement between experiments and simulations. Our results show that a physiological salt solution is a good solvent for αS and that the protein is highly dynamic throughout its entire chain, with local intra- and inter-regional interactions leading to deviations from global scaling. Specifically, we observe expansion in the C-terminal region, compaction in the NAC region, and a slightly smaller distance between the C- and N-termini than expected. Our simulations indicate that the compaction in the NAC region results from hydrophobic aliphatic contacts, mostly between valine and alanine residues, and cation-π interactions between lysine and tyrosine. In addition, hydrogen bonds also seem to contribute to the compaction of the NAC region. The expansion of the C-terminal region is due to intraregional electrostatic repulsion and increased chain stiffness from several prolines. Overall, our study demonstrates the effectiveness of combining smFRET experiments with CG-MD simulations to investigate the key interactions in highly dynamic IDPs at the amino acid level.
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Affiliation(s)
- Gobert Heesink
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mirjam J. Marseille
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mohammad A. A. Fakhree
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mark D. Driver
- Micromechanics,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kirsten A. van Leijenhorst-Groener
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Patrick R. Onck
- Micromechanics,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Christian Blum
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M.A.E. Claessens
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
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24
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Jacob MH, D’Souza RN, Lazar AI, Nau WM. Diffusion-Enhanced Förster Resonance Energy Transfer in Flexible Peptides: From the Haas-Steinberg Partial Differential Equation to a Closed Analytical Expression. Polymers (Basel) 2023; 15:polym15030705. [PMID: 36772006 PMCID: PMC9919848 DOI: 10.3390/polym15030705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In the huge field of polymer structure and dynamics, including intrinsically disordered peptides, protein folding, and enzyme activity, many questions remain that cannot be answered by methodology based on artificial intelligence, X-ray, or NMR spectroscopy but maybe by fluorescence spectroscopy. The theory of Förster resonance energy transfer (FRET) describes how an optically excited fluorophore transfers its excitation energy through space to an acceptor moiety-with a rate that depends on the distance between donor and acceptor. When the donor and acceptor moiety are conjugated to different sites of a flexible peptide chain or any other linear polymer, the pair could in principle report on chain structure and dynamics, on the site-to-site distance distribution, and on the diffusion coefficient of mutual site-to-site motion of the peptide chain. However, the dependence of FRET on distance distribution and diffusion is not defined by a closed analytical expression but by a partial differential equation (PDE), by the Haas-Steinberg equation (HSE), which can only be solved by time-consuming numerical methods. As a second complication, time-resolved FRET measurements have thus far been deemed necessary. As a third complication, the evaluation requires a computationally demanding but indispensable global analysis of an extended experimental data set. These requirements have made the method accessible to only a few experts. Here, we show how the Haas-Steinberg equation leads to a closed analytical expression (CAE), the Haas-Steinberg-Jacob equation (HSJE), which relates a diffusion-diagnosing parameter, the effective donor-acceptor distance, to the augmented diffusion coefficient, J, composed of the diffusion coefficient, D, and the photophysical parameters that characterize the used FRET method. The effective donor-acceptor distance is easily retrieved either through time-resolved or steady-state fluorescence measurements. Any global fit can now be performed in seconds and minimizes the sum-of-square difference between the experimental values of the effective distance and the values obtained from the HSJE. In summary, the HSJE can give a decisive advantage in applying the speed and sensitivity of FRET spectroscopy to standing questions of polymer structure and dynamics.
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25
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Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525885. [PMID: 36789411 PMCID: PMC9928041 DOI: 10.1101/2023.01.27.525885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Here, we introduce FRETpredict, a Python software program to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses an established Rotamer Library Approach to describe the FRET probes covalently bound to the protein. The software efficiently operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We demonstrate the performance and accuracy of the software for different types of systems: a relatively structured peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). We also describe a general approach to generate new rotamer libraries for FRET probes of interest. FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict.
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Affiliation(s)
- Daniele Montepietra
- Department of Physics, Computer Science and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A 41125 Modena, Italy
- Istituto Nanoscienze – CNR-NANO, Center S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - João M. Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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26
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Jin Z, Ling C, Li Y, Zhou J, Li K, Yim W, Yeung J, Chang YC, He T, Cheng Y, Fajtová P, Retout M, O'Donoghue AJ, Jokerst JV. Spacer Matters: All-Peptide-Based Ligand for Promoting Interfacial Proteolysis and Plasmonic Coupling. NANO LETTERS 2022; 22:8932-8940. [PMID: 36346642 DOI: 10.1021/acs.nanolett.2c03052] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plasmonic coupling via nanoparticle assembly is a popular signal-generation method in bioanalytical sensors. Here, we customized an all-peptide-based ligand that carries an anchoring group, polyproline spacer, biomolecular recognition, and zwitterionic domains for functionalizing gold nanoparticles (AuNPs) as a colorimetric enzyme sensor. Our results underscore the importance of the polyproline module, which enables the SARS-CoV-2 main protease (Mpro) to recognize the peptidic ligand on nanosurfaces for subsequent plasmonic coupling via Coulombic interactions. AuNP aggregation is favored by the lowered surface potential due to enzymatic unveiling of the zwitterionic module. Therefore, this system provides a naked-eye measure for Mpro. No proteolysis occurs on AuNPs modified with a control ligand lacking a spacer domain. Overall, this all-peptide-based ligand does not require complex molecular conjugations and hence offers a simple and promising route for plasmonic sensing other proteases.
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Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Chuxuan Ling
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Ke Li
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research, Singapore 138634
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Justin Yeung
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Yu-Ci Chang
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Yong Cheng
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Maurice Retout
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
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27
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Jacobi R, Hernández-Castillo D, Sinambela N, Bösking J, Pannwitz A, González L. Computation of Förster Resonance Energy Transfer in Lipid Bilayer Membranes. J Phys Chem A 2022; 126:8070-8081. [PMID: 36260519 PMCID: PMC9639162 DOI: 10.1021/acs.jpca.2c04524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Calculations of Förster
Resonance Energy Transfer (FRET)
often neglect the influence of different chromophore orientations
or changes in the spectral overlap. In this work, we present two computational
approaches to estimate the energy transfer rate between chromophores
embedded in lipid bilayer membranes. In the first approach, we assess
the transition dipole moments and the spectral overlap by means of
quantum chemical calculations in implicit solvation, and we investigate
the alignment and distance between the chromophores in classical molecular
dynamics simulations. In the second, all properties are evaluated
integrally with hybrid quantum mechanical/molecular mechanics (QM/MM)
calculations. Both approaches come with advantages and drawbacks,
and despite the fact that they do not agree quantitatively, they provide
complementary insights on the different factors that influence the
FRET rate. We hope that these models can be used as a basis to optimize
energy transfers in nonisotropic media.
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Affiliation(s)
- Richard Jacobi
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090Vienna, Austria.,Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Straße 42, 1090Vienna, Austria
| | - David Hernández-Castillo
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090Vienna, Austria.,Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Straße 42, 1090Vienna, Austria
| | - Novitasari Sinambela
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081Ulm, Germany
| | - Julian Bösking
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081Ulm, Germany
| | - Andrea Pannwitz
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081Ulm, Germany
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090Vienna, Austria.,Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, 1090Vienna, Austria
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28
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Rowling PJE, Murton BL, Du Z, Itzhaki LS. Multivalent Interaction of Beta-Catenin With its Intrinsically Disordered Binding Partner Adenomatous Polyposis Coli. Front Mol Biosci 2022; 9:896493. [PMID: 35755812 PMCID: PMC9214244 DOI: 10.3389/fmolb.2022.896493] [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: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The Wnt signalling pathway plays key roles in cell proliferation, differentiation and fate decisions in embryonic development and maintenance of adult tissues, and the twelve Armadillo (ARM) repeat-containing protein β-catenin acts as the signal transducer in this pathway. Here we investigate the interaction between β-catenin's ARM repeat domain and the intrinsically disordered protein adenomatous polyposis coli (APC). APC is a giant multivalent scaffold that brings together the different components of the so-called "β-catenin destruction complex", which drives β-catenin degradation via the ubiquitin-proteasome pathway. Mutations and truncations in APC, resulting in loss of APC function and hence elevated β-catenin levels and upregulation of Wnt signalling, are associated with numerous cancers including colorectal carcinomas. APC has a long intrinsically disordered region (IDR) that contains a series of 15-residue and 20-residue binding regions for β-catenin. Here we explore the multivalent nature of the interaction of β-catenin with the highest affinity APC repeat, both at equilibrium and under kinetic conditions. We use a combination of single-site substitutions, deletions and insertions to dissect the mechanism of molecular recognition and the roles of the three β-catenin-binding subdomains of APC.
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Affiliation(s)
| | | | | | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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29
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Barth A, Opanasyuk O, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CAM. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. J Chem Phys 2022; 156:141501. [PMID: 35428384 PMCID: PMC9014241 DOI: 10.1063/5.0089134] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/31/2023] Open
Abstract
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E-τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.
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Affiliation(s)
- Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Thomas-Otavio Peulen
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, USA
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
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30
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Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022; 61:e202200119. [PMID: 35088931 DOI: 10.1002/anie.202200119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 12/26/2022]
Abstract
Functionalizable synthetic molecules with nanometer sizes and defined shapes in water are useful as molecular scaffolds to mimic the functions of biomacromolecules and develop chemical tools for manipulating biomacromolecules. Herein, we propose oligo(N-methylalanine) (oligo-NMA) as a peptide-based molecular scaffold with a minimal structure and a high density of functionalizable sites. Oligo-NMA forms a defined shape in water without hydrogen-bonding networks or ring constraints, which enables the molecule to act as a scaffold with minimal atomic composition. Furthermore, functional groups can be readily introduced on the nitrogens and α-carbons of oligo-NMA. Computational and NMR spectroscopic analysis suggested that the backbone structure of oligo-NMA is not largely affected by functionalization. Moreover, the usefulness of oligo-NMA was demonstrated by the design of protein ligands. The ease of synthesis, minimal structure, and high functionalization flexibility makes oligo-NMA a useful scaffold for chemical and biological applications.
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Affiliation(s)
- Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yota Shiratori
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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31
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Hu Y, Tian ZY, Xiong W, Wang D, Zhao R, Xie Y, Song YQ, Zhu J, Lu H. Water-Assisted and Protein-Initiated Fast and Controlled Ring-Opening Polymerization of Proline N-Carboxyanhydride. Natl Sci Rev 2022; 9:nwac033. [PMID: 36072505 PMCID: PMC9438472 DOI: 10.1093/nsr/nwac033] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/29/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
The production of polypeptides via the ring-opening polymerization (ROP) of N-carboxyanhydride (NCA) is usually conducted under stringent anhydrous conditions. The ROP of proline NCA (ProNCA) for the synthesis of poly-L-proline (PLP) is particularly challenging due to the premature product precipitation as polyproline type I helices, leading to slow reactions for up to one week, poor control of the molar mass and laborious workup. Here, we report the unexpected water-assisted controlled ROP of ProNCA, which affords well-defined PLP as polyproline II helices in 2–5 minutes and almost-quantitative yields. Experimental and theoretical studies together suggest the as-yet-unreported role of water in facilitating proton shift, which significantly lowers the energy barrier of the chain propagation. The scope of initiators can be expanded from hydrophobic amines to encompass hydrophilic amines and thiol-bearing nucleophiles, including complex biomacromolecules such as proteins. Protein-mediated ROP of ProNCA conveniently affords various protein-PLP conjugates via a grafting-from approach. PLP modification not only preserves the biological activities of the native proteins, but also enhances their resistance to extreme conditions. Moreover, PLP modification extends the elimination half-life of asparaginase (ASNase) 18-fold and mitigates the immunogenicity of wt ASNase >250-fold (ASNase is a first-line anticancer drug for lymphoma treatment). This work provides a simple solution to a long-standing problem in PLP synthesis, and offers valuable guidance for the development of water-resistant ROP of other proline-like NCAs. The facile access to PLP can greatly boost the application potential of PLP-based functional materials for engineering industry enzymes and therapeutic proteins.
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Affiliation(s)
- Yali Hu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Zi-You Tian
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Wei Xiong
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Dedao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing100142, China
| | - Ruichi Zhao
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Yan Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing100142, China
| | - Yu-Qin Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing100142, China
| | - Jun Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing100142, China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
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32
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He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022; 2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg2+ cations stabilizes the compact state. The absence of Mg2+ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, United States
| | - Anja Henning-Knechtel
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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33
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Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Marin Yokomine
- The University of Tokyo: Tokyo Daigaku Department of Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Jumpei Morimoto
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Yasuhiro Fukuda
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnolgy 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Yota Shiratori
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Daisuke Kuroda
- The University of Tokyo: Tokyo Daigaku Bioengineering 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Takumi Ueda
- The University of Tokyo: Tokyo Daigaku Graduate school of pharmaceutical sciences 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo JAPAN
| | - Koh Takeuchi
- The University of Tokyo: Tokyo Daigaku Graduate school of pharmaceutical sciences 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo JAPAN
| | - Kouhei Tsumoto
- The University of Tokyo: Tokyo Daigaku Institute of medical science 4-6-1, Shirokanedai, Minato-ku 108-8639 Tokyo JAPAN
| | - Shinsuke Sando
- The University of Tokyo Department of Chemistry and Biotechnology, Graduate School of Engineering Hongo 7-3-1, Bunkyo-ku 113-8656 Tokyo JAPAN
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34
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Gopich IV, Chung HS. Theory and Analysis of Single-Molecule FRET Experiments. Methods Mol Biol 2022; 2376:247-282. [PMID: 34845614 DOI: 10.1007/978-1-0716-1716-8_14] [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: 06/13/2023]
Abstract
Inter-dye distances and conformational dynamics can be studied using single-molecule FRET measurements. We consider two approaches to analyze sequences of photons with recorded photon colors and arrival times. The first approach is based on FRET efficiency histograms obtained from binned photon sequences. The experimental histograms are compared with the theoretical histograms obtained using the joint distribution of acceptor and donor photons or the Gaussian approximation. In the second approach, a photon sequence is analyzed without binning. The parameters of a model describing conformational dynamics are found by maximizing the appropriate likelihood function. The first approach is simpler, while the second one is more accurate, especially when the population of species is small and transition rates are fast. The likelihood-based analysis as well as the recoloring method has the advantage that diffusion of molecules through the laser focus can be rigorously handled.
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Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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35
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Naudi-Fabra S, Tengo M, Jensen MR, Blackledge M, Milles S. Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS. J Am Chem Soc 2021; 143:20109-20121. [PMID: 34817999 PMCID: PMC8662727 DOI: 10.1021/jacs.1c06264] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/18/2022]
Abstract
Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and only accessible to a few solution state techniques, such as nuclear magnetic resonance (NMR), small-angle scattering techniques, and single-molecule Förster resonance energy transfer (smFRET). While each of the techniques is sensitive to different properties of the disordered chain, such as local structural propensities, overall dimension, or intermediate- and long-range contacts, conformational ensembles describing intrinsically disordered proteins (IDPs) accurately should ideally respect all of these properties. Here we develop an integrated approach using a large set of FRET efficiencies and fluorescence lifetimes, NMR chemical shifts, and paramagnetic relaxation enhancements (PREs), as well as small-angle X-ray scattering (SAXS) to derive quantitative conformational ensembles in agreement with all parameters. Our approach is tested using simulated data (five sets of PREs and 15 FRET efficiencies) and validated experimentally on the example of the disordered domain of measles virus phosphoprotein, providing new insights into the conformational landscape of this viral protein that comprises transient structural elements and is more compact than an unfolded chain throughout its length. Rigorous cross-validation using FRET efficiencies, fluorescence lifetimes, and SAXS demonstrates the predictive nature of the calculated conformational ensembles and underlines the potential of this strategy in integrative dynamic structural biology.
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Affiliation(s)
- Samuel Naudi-Fabra
- Institut de Biologie Structurale,
Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Maud Tengo
- Institut de Biologie Structurale,
Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale,
Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale,
Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Sigrid Milles
- Institut de Biologie Structurale,
Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38044 Grenoble, France
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36
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Klose D, Holla A, Gmeiner C, Nettels D, Ritsch I, Bross N, Yulikov M, Allain FHT, Schuler B, Jeschke G. Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries. Biophys J 2021; 120:4842-4858. [PMID: 34536387 PMCID: PMC8595751 DOI: 10.1016/j.bpj.2021.09.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
Förster resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) spectroscopy are complementary techniques for quantifying distances in the nanometer range. Both approaches are commonly employed for probing the conformations and conformational changes of biological macromolecules based on site-directed fluorescent or paramagnetic labeling. FRET can be applied in solution at ambient temperature and thus provides direct access to dynamics, especially if used at the single-molecule level, whereas EPR requires immobilization or work at cryogenic temperatures but provides data that can be more reliably used to extract distance distributions. However, a combined analysis of the complementary data from the two techniques has been complicated by the lack of a common modeling framework. Here, we demonstrate a systematic analysis approach based on rotamer libraries for both FRET and EPR labels to predict distance distributions between two labels from a structural model. Dynamics of the fluorophores within these distance distributions are taken into account by diffusional averaging, which improves the agreement with experiment. Benchmarking this methodology with a series of surface-exposed pairs of sites in a structured protein domain reveals that the lowest resolved distance differences can be as small as ∼0.25 nm for both techniques, with quantitative agreement between experimental and simulated transfer efficiencies within a range of ±0.045. Rotamer library analysis thus establishes a coherent way of treating experimental data from EPR and FRET and provides a basis for integrative structural modeling, including studies of conformational distributions and dynamics of biological macromolecules using both techniques.
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Affiliation(s)
- Daniel Klose
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Christoph Gmeiner
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Irina Ritsch
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nadja Bross
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Physics, University of Zurich, Zurich, Switzerland.
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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37
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Das D, Arora L, Mukhopadhyay S. Fluorescence Depolarization Kinetics Captures Short-Range Backbone Dihedral Rotations and Long-Range Correlated Dynamics of an Intrinsically Disordered Protein. J Phys Chem B 2021; 125:9708-9718. [PMID: 34415768 DOI: 10.1021/acs.jpcb.1c04426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not autonomously fold into well-defined three-dimensional structures and are best described as a heterogeneous ensemble of rapidly interconverting conformers. It is challenging to elucidate their complex dynamic signatures using a single technique. In this study, we employed sensitive fluorescence depolarization kinetics by following picosecond time-resolved fluorescence anisotropy decays to directly capture the essential dynamical features of intrinsically disordered α-synuclein (α-syn) site-specifically labeled with thiol-active fluorophores. By utilizing a long-lifetime (≥10 ns) anisotropic label, we were able to discern three distinct rotational components of α-syn. The subnanosecond component represents the local wobbling-in-cone motion of the fluorophore, whereas the slower (∼1.4 ns) component corresponds to the short-range backbone dynamics governed by collective torsional fluctuations in the Ramachandran Φ-Ψ dihedral space. This backbone dihedral rotational time scale is sensitive to the local chain stiffness and slows down in the presence of an adjacent proline residue. We also observed a small-amplitude (≤10%) slower rotational correlation time (6-10 ns) that represents the long-range correlated dynamics involving a much longer segment of the polypeptide chain. These intrinsic dynamic signatures of IDPs will provide critical mechanistic underpinnings in a mosaic of biophysical phenomena involving internal friction, allosteric interactions, and phase separation.
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38
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Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021; 193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
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39
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Li RS, Liu J, Yan Y, Su C, Lai T, Liao Y, Li YF, Li N, Huang CZ. Aggregation-Enhanced Energy Transfer for Mitochondria-Targeted ATP Ratiometric Imaging in Living Cells. Anal Chem 2021; 93:11878-11886. [PMID: 34403238 DOI: 10.1021/acs.analchem.1c02833] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Förster resonance energy transfer (FRET) from fluorescent nanoparticles to fluorescent dyes is an attractive approach for bioanalysis in living cells. However, the luminescence of the nanoparticle donor/acceptor has not been effectively used to produce highly efficient FRET because the distance between the energy donor and energy acceptor is often larger than the effective FRET radius (about 10 nm) and the uncontrolled rotational and translational diffusion of luminophores. Here, we develop an aggregation-enhanced energy transfer strategy that can overcome the impedance for effective energy transfer. The functional nanoprobes, named TPP-CDs-FITC, are carbon dots (CDs) functionalized with triphenylphosphine (TPP) and ∼117 fluorescein 5-isothiocyanate (FITC) on the surface. In dispersed solution, the 3.8 nm TPP-CDs-FITC show weak FRET efficiency (15.4%). After TPP-instructed mitochondrial targeting, enhanced FRET efficiency (53.2%) is induced due to the aggregation of TPP-CDs-FITC selectively triggered by adenosine triphosphate (ATP) in the mitochondria. The enhanced FRET efficiency can be attributed to the joint effect of the augment of numbers of FITC acceptors within 10 nm from dispersed 117 to aggregated 5499 and the restricted rotational and translational motions of TPP-CDs donors and FITC acceptors. Ultimately, we successfully observe the fluctuations of ATP levels in the mitochondria using the aggregation-enhanced energy transfer strategy of the TPP-CDs-FITC nanodevice.
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Affiliation(s)
- Rong Sheng Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.,Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, China
| | - Jiahui Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuan Yan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chuanyang Su
- General Station for Drug & Instrument Supervision and Control Joint Logistics Support Force, PLA, Beijing 100071, China
| | - Tiancheng Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yunwen Liao
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, China
| | - Yuan Fang Li
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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40
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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41
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Mondal S, Mondal S, Seki K, Bagchi B. An exact solution in the theory of fluorescence resonance energy transfer with vibrational relaxation. J Chem Phys 2021; 154:134104. [PMID: 33832249 DOI: 10.1063/5.0045008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The elegant expression of Förster that predicts the well-known 1/R6 distance (R) dependence of the rate of energy transfer, although widely used, was derived using several approximations. Notable among them is the neglect of the vibrational relaxation in the reactant (donor) and product (acceptor) manifolds. Vibrational relaxation can play an important role when the energy transfer rate is faster than the vibrational relaxation rate. Under such conditions, donor to acceptor energy transfer can occur from the excited vibrational states. This phenomenon is not captured by the usual formulation based on the overlap of donor emission and acceptor absorption spectra. Here, we develop a Green's function-based generalized formalism and obtain an exact solution for the excited state population relaxation and the rate of energy transfer in the presence of vibrational relaxation. We find that the application of the well-known Förster's expression might lead to overestimation of R.
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Affiliation(s)
- Sangita Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, India
| | - Kazuhiko Seki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, India
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42
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021; 7:eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.
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Affiliation(s)
| | - Joseph W F Robertson
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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43
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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44
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Panniello A, Trapani M, Cordaro M, Dibenedetto CN, Tommasi R, Ingrosso C, Fanizza E, Grisorio R, Collini E, Agostiano A, Curri ML, Castriciano MA, Striccoli M. High-Efficiency FRET Processes in BODIPY-Functionalized Quantum Dot Architectures. Chemistry 2021; 27:2371-2380. [PMID: 32896940 DOI: 10.1002/chem.202003574] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 01/24/2023]
Abstract
Efficient FRET systems are developed combining colloidal CdSe quantum dots (QDs) donors and BODIPY acceptors. To promote effective energy transfer in FRET architectures, the distance between the organic fluorophore and the QDs needs to be optimized by a careful system engineering. In this context, BODIPY dyes bearing amino-terminated functionalities are used in virtue of the high affinity of amine groups in coordinating the QD surface. A preliminary QD surface treatment with a short amine ligand is performed to favor the interaction with the organic fluorophores in solution. The successful coordination of the dye to the QD surface, accomplishing a short donor-acceptor distance, provides effective energy transfer already in solution, with efficiency of 76 %. The efficiency further increases in the solid state where the QDs and the dye are deposited as single coordinated units from solution, with a distance between the fluorophores down to 2.2 nm, demonstrating the effectiveness of the coupling strategy.
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Affiliation(s)
- Annamaria Panniello
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Mariachiara Trapani
- Istituto per lo Studio dei Materiali Nanostrutturati del CNR (ISMN-CNR), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Massimiliano Cordaro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Carlo Nazareno Dibenedetto
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Raffaele Tommasi
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy
| | - Chiara Ingrosso
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Elisabetta Fanizza
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Roberto Grisorio
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di, Chimica (DICATECh), Politecnico di Bari, Via Orabona, 4, 70126, Bari, Italy
| | - Elisabetta Collini
- Dipartimento Scienze Chimiche, Università di Padova, via Marzolo 1, 35131, Padova, Italy
| | - Angela Agostiano
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Maria Lucia Curri
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Maria Angela Castriciano
- Istituto per lo Studio dei Materiali Nanostrutturati del CNR (ISMN-CNR), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Marinella Striccoli
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
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45
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Schepers B, Gohlke H. AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools. J Chem Phys 2021; 152:221103. [PMID: 32534525 DOI: 10.1063/5.0007630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Molecular dynamics (MD) simulations of explicit representations of fluorescent dyes attached via a linker to a protein allow, e.g., probing commonly used approximations for dye localization and/or orientation or modeling Förster resonance energy transfer. However, setting up and performing such MD simulations with the AMBER suite of biomolecular simulation programs has remained challenging due to the unavailability of an easy-to-use set of parameters within AMBER. Here, we adapted the AMBER-DYES parameter set derived by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] into "AMBER-DYES in AMBER" to generate a force field applicable within AMBER for commonly used fluorescent dyes and linkers attached to a protein. In particular, the computationally efficient graphics processing unit (GPU) implementation of the AMBER MD engine can now be exploited to overcome sampling issues of dye movements. The implementation is compatible with state-of-the-art force fields such as GAFF, GAFF2, ff99SB, ff14SB, lipid17, and GLYCAM_06j, which allows simulating post-translationally modified proteins and/or protein-ligand complexes and/or proteins in membrane environments. It is applicable with frequently used water models such as TIP3P, TIP4P, TIP4P-Ew, and OPC. For ease of use, a LEaP-based workflow was created, which allows attaching (multiple) dye/linker combinations to a protein prior to further system preparation steps. Following the parameter development described by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] and the adaptation steps described here, AMBER-DYES in AMBER can be extended by additional linkers and fluorescent molecules.
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Affiliation(s)
- Bastian Schepers
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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46
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Li D, Ren J, Ji F, Peng Q, Teng H, Jia L. Peptide Linker Affecting the Activity Retention Rate of VHH in Immunosorbents. Biomolecules 2020; 10:biom10121610. [PMID: 33261088 PMCID: PMC7760621 DOI: 10.3390/biom10121610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
VHH-based immunosorbents are an emerging and promising tool for the removal of toxic substances from plasma. However, the small size of VHHs is a double-edged sword, bringing both benefits and drawbacks to the immunosorbent. The small size of the VHH allows a higher coupling density, while the closer distance to the resin might create steric hindrance for paratope access. The latter could be avoided by inserting a linker between the VHH and the gel attachment site. Here, we report an approach to improve the activity retention of the immobilized VHH by selecting suitable linkers between the VHH and the site-specific immobilization site on the resin. Seven peptide linkers differing in length and flexibility were fused to the VHH and contained the formylglycine generating enzyme (FGE) recognition sequence. These constructs were expressed in the cytoplasm of bacteria and purified, the VHH production yield and affinity for its cognate antigen was measured. Furthermore, the fGly conversion, the immobilization of the aldehyde-containing nanobodies, the immobilization on resin and the antigen binding activity of the VHH-based immunoadsorbents was monitored. The VHH with longer and rigid, proline-rich linkers exhibited good expression yield of approximately 160 mg/L of culture, a fGly conversion of up to 100%, and the highest activity retention rate of more than 68%. This study unveiled two suitable linkers for the preparation of VHH-based immunosorbents that will assist the development of their clinical application.
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47
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Sherck N, Webber T, Brown DR, Keller T, Barry M, DeStefano A, Jiao S, Segalman RA, Fredrickson GH, Shell MS, Han S. End-to-End Distance Probability Distributions of Dilute Poly(ethylene oxide) in Aqueous Solution. J Am Chem Soc 2020; 142:19631-19641. [DOI: 10.1021/jacs.0c08709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Timothy Keller
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Glenn H. Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Materials, University of California, Santa Barbara, California 93106, United States
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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48
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Morató A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernadó P. Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins. Biomolecules 2020; 10:E1458. [PMID: 33086646 PMCID: PMC7603387 DOI: 10.3390/biom10101458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022] Open
Abstract
The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.
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Affiliation(s)
| | | | | | | | | | | | | | - Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
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49
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Yang L, Jang SJ. Theoretical investigation of non-Förster exciton transfer mechanisms in perylene diimide donor, phenylene bridge, and terrylene diimide acceptor systems. J Chem Phys 2020; 153:144305. [PMID: 33086841 DOI: 10.1063/5.0023709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rates of exciton transfer within dyads of perylene diimide and terrylene diimide connected by oligophenylene bridge units have been shown to deviate significantly from those of Förster's resonance energy transfer theory, according to single molecule spectroscopy experiments. The present work provides a detailed computational and theoretical study investigating the source of such a discrepancy. Electronic spectroscopy data are calculated by time-dependent density functional theory and then compared with experimental results. Electronic couplings between the exciton donor and the acceptor are estimated based on both the transition density cube method and transition dipole approximation. These results confirm that the delocalization of the exciton to the bridge parts contributes to significant enhancement of donor-acceptor electronic coupling. Mechanistic details of exciton transfer are examined by estimating the contributions of the bridge electronic states, vibrational modes of the dyads commonly coupled to both donor and acceptor, inelastic resonance energy transfer mechanism, and dark exciton states. These analyses suggest that the contribution of common vibrational modes serves as the main source of deviation from Förster's spectral overlap expression.
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Affiliation(s)
- Lei Yang
- Center for Molecular Systems and Organic Devices, Key Laboratory for Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, USA and PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, USA
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50
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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