1
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Pierro A, Bonucci A, Magalon A, Belle V, Mileo E. Impact of Cellular Crowding on Protein Structural Dynamics Investigated by EPR Spectroscopy. Chem Rev 2024; 124:9873-9898. [PMID: 39213496 DOI: 10.1021/acs.chemrev.3c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The study of how the intracellular medium influences protein structural dynamics and protein-protein interactions is a captivating area of research for scientists aiming to comprehend biomolecules in their native environment. As the cellular environment can hardly be reproduced in vitro, direct investigation of biomolecules within cells has attracted growing interest in the past two decades. Among magnetic resonances, site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) has emerged as a powerful tool for studying the structural properties of biomolecules directly in cells. Since the first in-cell EPR experiment was reported in 2010, substantial progress has been made, and this Review provides a detailed overview of the developments and applications of this spectroscopic technique. The strategies available for preparing a cellular sample and the EPR methods that can be applied to cells will be discussed. The array of spin labels available, along with their strengths and weaknesses in cellular contexts, will also be described. Several examples will illustrate how in-cell EPR can be applied to different biological systems and how the cellular environment affects the structural and dynamic properties of different proteins. Lastly, the Review will focus on the future developments expected to expand the capabilities of this promising technique.
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Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Alessio Bonucci
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Axel Magalon
- Aix Marseille University, CNRS, Laboratoire de Chimie Bactérienne (LCB), IMM, IM2B, Marseille, France
| | - Valérie Belle
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Elisabetta Mileo
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
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2
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Liu ZH, Tsanai M, Zhang O, Forman-Kay J, Head-Gordon T. Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes. ARXIV 2024:arXiv:2409.02240v1. [PMID: 39279844 PMCID: PMC11398552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate structural and dynamic characteristics of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). Unlike crystallographic beamlines and their role in streamlining acquisition of structures for folded proteins, an integrated experimental and computational approach aimed at IDPs/IDRs has emerged. In this Perspective we aim to provide a robust overview of current computational tools for IDPs and IDRs, and most recently their complexes and phase separated states, including statistical models, physics-based approaches, and machine learning methods that permit structural ensemble generation and validation against many solution experimental data types.
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Affiliation(s)
- Zi Hao Liu
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Maria Tsanai
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | - Oufan Zhang
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | - Julie Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, USA
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3
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Martinho M, Allegro D, Etienne E, Lohberger C, Bonucci A, Belle V, Barbier P. Structural Flexibility of Tau in Its Interaction with Microtubules as Viewed by Site-Directed Spin Labeling EPR Spectroscopy. Methods Mol Biol 2024; 2754:55-75. [PMID: 38512660 DOI: 10.1007/978-1-0716-3629-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Tau is a microtubule-associated protein that belongs to the Intrinsically Disordered Proteins (IDPs) family. IDPs or Intrinsically Disordered Regions (IDRs) play key roles in protein interaction networks and their dysfunctions are often related to severe diseases. Defined by their lack of stable secondary and tertiary structures in physiological conditions while being functional, these proteins use their inherent structural flexibility to adapt to and interact with various binding partners. Knowledges on the structural dynamics of IDPs and their different conformers are crucial to finely decipher fundamental biological processes controlled by mechanisms such as conformational adaptations or switches, induced fit, or conformational selection events. Different mechanisms of binding have been proposed: among them, the so-called folding-upon-binding in which the IDP adopts a certain conformation upon interacting with a partner protein, or the formation of a "fuzzy" complex in which the IDP partly keeps its dynamical character at the surface of its partner. The dynamical nature and physicochemical properties of unbound as well as bound IDPs make this class of proteins particularly difficult to characterize by classical bio-structural techniques and require specific approaches for the fine description of their inherent dynamics.Among other techniques, Site-Directed Spin Labeling combined with Electron Paramagnetic Resonance (SDSL-EPR) spectroscopy has gained much interest in this last decade for the study of IDPs. SDSL-EPR consists in grafting a paramagnetic label (mainly a nitroxide radical) at selected site(s) of the macromolecule under interest followed by its observation using and/or combining different EPR strategies. These nitroxide spin labels detected by continuous wave (cw) EPR spectroscopy are used as perfect reporters or "spy spins" of their local environment, being able to reveal structural transitions, folding/unfolding events, etc. Another approach is based on the measurement of inter-label distance distributions in the 1.5-8.0 nm range using pulsed dipolar EPR experiments, such as Double Electron-Electron Resonance (DEER) spectroscopy. The technique is then particularly well suited to study the behavior of Tau in its interaction with its physiological partner: microtubules (MTs). In this chapter we provide a detailed experimental protocol for the labeling of Tau protein and its EPR study while interacting with preformed (Paclitaxel-stabilized) MTs, or using Tau as MT inducer. We show how the choice of nitroxide label can be crucial to obtain functional information on Tau/tubulin complexes.
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Affiliation(s)
| | - Diane Allegro
- Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | | | - Cynthia Lohberger
- Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | | | | | - Pascale Barbier
- Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France.
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4
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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5
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Vanas A, Soetbeer J, Breitgoff FD, Hintz H, Sajid M, Polyhach Y, Godt A, Jeschke G, Yulikov M, Klose D. Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing). MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:1-18. [PMID: 38269110 PMCID: PMC10807728 DOI: 10.5194/mr-4-1-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/14/2022] [Indexed: 01/26/2024]
Abstract
To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin S = 1 / 2 . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.
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Affiliation(s)
- Agathe Vanas
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Frauke Diana Breitgoff
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Henrik Hintz
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Muhammad Sajid
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
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6
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Georgieva E, Karamalakova Y, Arabadzhiev G, Atanasov V, Kostandieva R, Mitev M, Tsoneva V, Yovchev Y, Nikolova G. Site-Directed Spin Labeling EPR Spectroscopy for Determination of Albumin Structural Damage and Hypoalbuminemia in Critical COVID-19. Antioxidants (Basel) 2022; 11:antiox11122311. [PMID: 36552520 PMCID: PMC9774111 DOI: 10.3390/antiox11122311] [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: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
The main factors in the COVID-19 pathology, which can initiate extensive structural changes at the cellular and molecular levels, are the generation of free radicals in abnormal amounts, and oxidative stress. Under "oxidative shock" conditions, the proteins undergo various modifications that affect their function and activity, and as a result distribute malfunctioning protein derivatives in the body. Human serum albumin is a small globular protein characterized by a high overall binding capacity for neutral lipophilic and acidic dosage forms. The albumin concentration is crucial for the maintenance of plasma oncotic pressure, the transport of nutrients, amino acids, and drugs, the effectiveness of drug therapy, and the prevention of drug toxicity. Hypoalbuminemia and structural defects molecule in the protein suggest a risk of changed metabolism and increased plasma concentration of unbound drugs. Therefore, the albumin structural and functional changes accompanied by low protein levels can be a serious prerequisite for ineffective therapy, frequent complications, and high mortality in patients with SARS-CoV-2 infection. The current opinion aims the research community the application of Site-Directed Spin Labeling Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) and 3-Maleimido-PROXYL radical in determining abnormalities of the albumin dynamics and protein concentrations in COVID-19 critical patients.
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Affiliation(s)
- Ekaterina Georgieva
- Department of “General and Clinical Pathology, Forensic Medicine, Deontology and Dermatovenerology”, Medical Faculty, Trakia University, 11 Armeiska Str., 6000 Stara Zagora, Bulgaria
- Department of “Medical Chemistry and Biochemistry”, Medical Faculty, Trakia University, 11 Armeiska Str., 6000 Stara Zagora, Bulgaria
| | - Yanka Karamalakova
- Department of “Medical Chemistry and Biochemistry”, Medical Faculty, Trakia University, 11 Armeiska Str., 6000 Stara Zagora, Bulgaria
| | - Georgi Arabadzhiev
- Department of “Surgery and Anesthesiology”, University Hospital “Prof. Dr. St. Kirkovich”, 6000 Stara Zagora, Bulgaria
| | - Vasil Atanasov
- Forensic Toxicology Laboratory, Military Medical Academy, 3 “Sv. Georgi Sofiiski Str.”, 1606 Sofia, Bulgaria
| | - Rositsa Kostandieva
- Forensic Toxicology Laboratory, Military Medical Academy, 3 “Sv. Georgi Sofiiski Str.”, 1606 Sofia, Bulgaria
| | - Mitko Mitev
- Department of “Diagnostic Imaging”, University Hospital “Prof. Dr. St. Kirkovich”, 6000 Stara Zagora, Bulgaria
| | - Vanya Tsoneva
- Department of Propaedeutics of Internal Medicine and Clinical Laboratory, Medical Faculty, Trakia University, 11 Armeiska Str., 6000 Stara Zagora, Bulgaria
| | - Yovcho Yovchev
- Department of “Surgery and Anesthesiology”, University Hospital “Prof. Dr. St. Kirkovich”, 6000 Stara Zagora, Bulgaria
| | - Galina Nikolova
- Department of “Medical Chemistry and Biochemistry”, Medical Faculty, Trakia University, 11 Armeiska Str., 6000 Stara Zagora, Bulgaria
- Correspondence: ; Tel.: +359-897771301
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7
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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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8
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Selvaraj C, Pravin MA, Alhoqail WA, Nayarisseri A, Singh SK. Intrinsically disordered proteins in viral pathogenesis and infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:221-242. [PMID: 36088077 DOI: 10.1016/bs.apcsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Disordered proteins serve a crucial part in many biological processes that go beyond the capabilities of ordered proteins. A large number of virus-encoded proteins have extremely condensed proteomes and genomes, which results in highly disordered proteins. The presence of these IDPs allows them to rapidly adapt to changes in their biological environment and play a significant role in viral replication and down-regulation of host defense mechanisms. Since viruses undergo rapid evolution and have a high rate of mutation and accumulation in their proteome, IDPs' insights into viruses are critical for understanding how viruses hijack cells and cause disease. There are many conformational changes that IDPs can adopt in order to interact with different protein partners and thus stabilize the particular fold and withstand high mutation rates. This chapter explains the molecular mechanism behind viral IDPs, as well as the significance of recent research in the field of IDPs, with the goal of gaining a deeper comprehension of the essential roles and functions played by viral proteins.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Wardah A Alhoqail
- Department of Biology, College of Education, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Anuraj Nayarisseri
- In Silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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9
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Gracia P, Polanco D, Tarancón-Díez J, Serra I, Bracci M, Oroz J, Laurents DV, García I, Cremades N. Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau. Nat Commun 2022; 13:4586. [PMID: 35933508 PMCID: PMC9357037 DOI: 10.1038/s41467-022-32350-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
Amyloid aggregation of α-synuclein (αS) is the hallmark of Parkinson's disease and other synucleinopathies. Recently, Tau protein, generally associated with Alzheimer's disease, has been linked to αS pathology and observed to co-localize in αS-rich disease inclusions, although the molecular mechanisms for the co-aggregation of both proteins remain elusive. We report here that αS phase-separates into liquid condensates by electrostatic complex coacervation with positively charged polypeptides such as Tau. Condensates undergo either fast gelation or coalescence followed by slow amyloid aggregation depending on the affinity of αS for the poly-cation and the rate of valence exhaustion of the condensate network. By combining a set of advanced biophysical techniques, we have been able to characterize αS/Tau liquid-liquid phase separation and identified key factors that lead to the formation of hetero-aggregates containing both proteins in the interior of the liquid protein condensates.
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Affiliation(s)
- Pablo Gracia
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - David Polanco
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - Jorge Tarancón-Díez
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - Ilenia Serra
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
| | - Maruan Bracci
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
| | - Javier Oroz
- "Rocasolano" Institute for Physical Chemistry, CSIC, Serrano 119, Madrid, E-28006, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, CSIC, Serrano 119, Madrid, E-28006, Spain
| | - Inés García
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
- Centro Universitario de la Defensa, Academia General Militar, Ctra. de Huesca s/n, 50090, Zaragoza, Spain
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain.
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain.
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10
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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [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: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles-encounter complexes-lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)-which exhibits an unexpected, intrinsically highly dynamic behavior-is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á. Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A. Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
- Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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11
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Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
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Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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12
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Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100616. [PMID: 34888535 PMCID: PMC8654206 DOI: 10.1016/j.xcrp.2021.100616] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Department of Chemistry, Navajo Technical University, Chinle, AZ 86503, USA
| | | | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Erkang Ou
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - George L. Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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13
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Shapiro DM, Ney M, Eghtesadi SA, Chilkoti A. Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications. J Phys Chem B 2021; 125:6740-6759. [PMID: 34143622 DOI: 10.1021/acs.jpcb.1c01146] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.
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Affiliation(s)
- Daniel Mark Shapiro
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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14
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A combined NMR and EPR investigation on the effect of the disordered RGG regions in the structure and the activity of the RRM domain of FUS. Sci Rep 2020; 10:20956. [PMID: 33262375 PMCID: PMC7708983 DOI: 10.1038/s41598-020-77899-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023] Open
Abstract
Structural disorder represents a key feature in the mechanism of action of RNA-binding proteins (RBPs). Recent insights revealed that intrinsically disordered regions (IDRs) linking globular domains modulate their capability to interact with various sequences of RNA, but also regulate aggregation processes, stress-granules formation, and binding to other proteins. The FET protein family, which includes FUS (Fused in Sarcoma), EWG (Ewing Sarcoma) and TAF15 (TATA binding association factor 15) proteins, is a group of RBPs containing three different long IDRs characterized by the presence of RGG motifs. In this study, we present the characterization of a fragment of FUS comprising two RGG regions flanking the RNA Recognition Motif (RRM) alone and in the presence of a stem-loop RNA. From a combination of EPR and NMR spectroscopies, we established that the two RGG regions transiently interact with the RRM itself. These interactions may play a role in the recognition of stem-loop RNA, without a disorder-to-order transition but retaining high dynamics.
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15
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Babić N, Orio M, Peyrot F. Unexpected rapid aerobic transformation of 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical by cytochrome P450 in the presence of NADPH: Evidence against a simple reduction of the nitroxide moiety to the hydroxylamine. Free Radic Biol Med 2020; 156:144-156. [PMID: 32561320 DOI: 10.1016/j.freeradbiomed.2020.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/29/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
Aminoxyl radicals (nitroxides) are a class of compounds with important biomedical applications, serving as antioxidants, spin labels for proteins, spin probes of oximetry, pH, or redox status in electron paramagnetic resonance (EPR), or as contrast agents in magnetic resonance imaging (MRI). However, the fast reduction of the radical moiety in common tetramethyl-substituted cyclic nitroxides within cells, yielding diamagnetic hydroxylamines, limits their use in spectroscopic and imaging studies. In vivo half-lives of commonly used tetramethyl-substituted nitroxides span no more than a few minutes. Therefore, synthetic efforts have focused on enhancing the nitroxide stability towards reduction by varying the electronic and steric environment of the radical. Tetraethyl-substitution at alpha position to the aminoxyl function proved efficient in vitro against reduction by ascorbate or cytosolic extracts. Moreover, 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical (TEEPONE) was used successfully for tridimensional EPR and MRI in vivo imaging of mouse head, with a reported half-life of over 80 min. We decided to investigate the stability of tetraethyl-substituted piperidine nitroxides in the presence of hepatic microsomal fractions, since no detailed study of their "metabolic stability" at the molecular level had been reported despite examples of the use of these nitroxides in vivo. In this context, the rapid aerobic transformation of TEEPONE observed in the presence of rat liver microsomal fractions and NADPH was unexpected. Combining EPR, HPLC-HRMS, and DFT studies on a series of piperidine nitroxides - TEEPONE, 4-oxo-2,2,6,6-tetramethyl(piperidin-1-yloxyl) (TEMPONE), and 2,2,6,6-tetraethyl-4-hydroxy(piperidin-1-yloxyl) (TEEPOL), we propose that the rapid loss in paramagnetic character of TEEPONE is not due to reduction to hydroxylamine but is a consequence of carbon backbone modification initiated by hydrogen radical abstraction in alpha position to the carbonyl by the P450-Fe(V)=O species. Besides, hydrogen radical abstraction by P450 on ethyl substituents, leading to dehydrogenation or hydroxylation products, leaves the aminoxyl function intact but could alter the linewidth of the EPR signal and thus interfere with methods relying on measurement of this parameter (EPR oximetry).
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Affiliation(s)
- Nikola Babić
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, F-75006, Paris, France
| | - Maylis Orio
- Aix-Marseille Univ., CNRS, Centrale Marseille, ISm2, Marseille, France
| | - Fabienne Peyrot
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, F-75006, Paris, France; Sorbonne Université, Institut National Supérieur Du Professorat et de L'Éducation (INSPE) de L'Académie de Paris, F-75016, Paris, France.
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16
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Pierro A, Etienne E, Gerbaud G, Guigliarelli B, Ciurli S, Belle V, Zambelli B, Mileo E. Nickel and GTP Modulate Helicobacter pylori UreG Structural Flexibility. Biomolecules 2020; 10:E1062. [PMID: 32708696 PMCID: PMC7408563 DOI: 10.3390/biom10071062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
UreG is a P-loop GTP hydrolase involved in the maturation of nickel-containing urease, an essential enzyme found in plants, fungi, bacteria, and archaea. This protein couples the hydrolysis of GTP to the delivery of Ni(II) into the active site of apo-urease, interacting with other urease chaperones in a multi-protein complex necessary for enzyme activation. Whereas the conformation of Helicobacter pylori (Hp) UreG was solved by crystallography when it is in complex with two other chaperones, in solution the protein was found in a disordered and flexible form, defining it as an intrinsically disordered enzyme and indicating that the well-folded structure found in the crystal state does not fully reflect the behavior of the protein in solution. Here, isothermal titration calorimetry and site-directed spin labeling coupled to electron paramagnetic spectroscopy were successfully combined to investigate HpUreG structural dynamics in solution and the effect of Ni(II) and GTP on protein mobility. The results demonstrate that, although the protein maintains a flexible behavior in the metal and nucleotide bound forms, concomitant addition of Ni(II) and GTP exerts a structural change through the crosstalk of different protein regions.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
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17
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Lindemann WR, Mijalis AJ, Alonso JL, Borbat PP, Freed JH, Arnaout MA, Pentelute BL, Ortony JH. Conformational Dynamics in Extended RGD-Containing Peptides. Biomacromolecules 2020; 21:2786-2794. [PMID: 32469507 PMCID: PMC7388056 DOI: 10.1021/acs.biomac.0c00506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RGD is a prolific example of a tripeptide used in biomaterials for cell adhesion, but the potency of free or surface-bound RGD tripeptide is orders-of-magnitude less than the RGD domain within natural proteins. We designed a set of peptides with varying lengths, composed of fragments of fibronectin protein whose central three residues are RGD, in order to vary their conformational behavior without changing the binding site's chemical environment. With these peptides, we measure the conformational dynamics and transient structure of the active site. Our studies reveal how flanking residues affect conformational behavior and integrin binding. We find that disorder of the binding site is important to the potency of RGD peptides and that transient hydrogen bonding near the RGD site affects both the energy landscape roughness of the peptides and peptide binding. This phenomenon is independent of longer-range folding interactions and helps explain why short binding sequences, including RGD itself, do not fully replicate the integrin-targeting properties of extracellular matrix proteins. Our studies reinforce that peptide binding is a holistic event and fragments larger than those directly involved in binding should be considered in the design of peptide epitopes for functional biomaterials.
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Affiliation(s)
- William R Lindemann
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José L Alonso
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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18
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Weickert S, Wawrzyniuk M, John LH, Rüdiger SGD, Drescher M. The mechanism of Hsp90-induced oligomerizaton of Tau. SCIENCE ADVANCES 2020; 6:eaax6999. [PMID: 32201713 PMCID: PMC7069708 DOI: 10.1126/sciadv.aax6999] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/17/2019] [Indexed: 05/27/2023]
Abstract
Aggregation of the microtubule-associated protein Tau is a hallmark of Alzheimer's disease with Tau oligomers suspected as the most toxic agent. Tau is a client of the molecular chaperone Hsp90, although it is unclear whether and how the chaperone massages the structure of intrinsically disordered Tau. Using electron paramagnetic resonance, we extract structural information from the very broad conformational ensemble of Tau: Tau in solution is highly dynamic and polymorphic, although "paper clip"-shaped by long-range contacts. Interaction with Hsp90 promotes an open Tau conformation, which we identify as the molecular basis for the formation of small Tau oligomers by exposure of the aggregation-prone repeat domain to other Tau molecules. At the same time, formation of Tau fibrils is inhibited. We therefore provide the nanometer-scale zoom into chaperoning an amyloid client, highlighting formation of oligomers as the consequence of this biologically relevant interaction.
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Affiliation(s)
- S. Weickert
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - M. Wawrzyniuk
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - L. H. John
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - S. G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - M. Drescher
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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19
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New synthetic route to 2,2,6,6-tetraethylpiperidin-4-one: A key-intermediate towards tetraethyl nitroxides. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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21
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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22
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Entropy and Information within Intrinsically Disordered Protein Regions. ENTROPY 2019; 21:e21070662. [PMID: 33267376 PMCID: PMC7515160 DOI: 10.3390/e21070662] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-structure-function paradigm to IDRs and motivates the development of new methods to extract information from IDR sequences. We argue that the information in IDR sequences cannot be fully revealed through positional conservation, which largely measures stable structural contacts and interaction motifs. Instead, considerations of evolutionary conservation of molecular features can reveal the full extent of information in IDRs. Experimental quantification of the large conformational entropy of IDRs is challenging but can be approximated through the extent of conformational sampling measured by a combination of NMR spectroscopy and lower-resolution structural biology techniques, which can be further interpreted with simulations. Conformational entropy and other biophysical features can be modulated by post-translational modifications that provide functional advantages to IDRs by tuning their energy landscapes and enabling a variety of functional interactions and modes of regulation. The diverse mosaic of functional states of IDRs and their conformational features within complexes demands novel metrics of information, which will reflect the complicated sequence-conformational ensemble-function relationship of IDRs.
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23
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Widder P, Berner F, Summerer D, Drescher M. Double Nitroxide Labeling by Copper-Catalyzed Azide-Alkyne Cycloadditions with Noncanonical Amino Acids for Electron Paramagnetic Resonance Spectroscopy. ACS Chem Biol 2019; 14:839-844. [PMID: 30998314 PMCID: PMC6534342 DOI: 10.1021/acschembio.8b01111] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 01/17/2023]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling (SDSL) is an important tool to obtain long-range distance restraints for protein structural research. We here study a variety of azide- and alkyne-bearing noncanonical amino acids (ncAA) in terms of protein single- and double-incorporation efficiency via nonsense suppression, metabolic stability, yields of nitroxide labeling via copper-catalyzed [3 + 2] azide-alkyne cycloadditions (CuAAC), and spectroscopic properties in continuous-wave and double electron-electron resonance measurements. We identify para-ethynyl-l-phenylalanine and para-propargyloxy-l-phenylalanine as suitable ncAA for CuAAC-based SDSL that will complement current SDSL approaches, particularly in cases in which essential cysteines of a target protein prevent the use of sulfhydryl-reactive spin labels.
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Affiliation(s)
- Pia Widder
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Frederic Berner
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Summerer
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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24
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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25
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Martinho M, Allegro D, Huvent I, Chabaud C, Etienne E, Kovacic H, Guigliarelli B, Peyrot V, Landrieu I, Belle V, Barbier P. Two Tau binding sites on tubulin revealed by thiol-disulfide exchanges. Sci Rep 2018; 8:13846. [PMID: 30218010 PMCID: PMC6138654 DOI: 10.1038/s41598-018-32096-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/14/2018] [Indexed: 01/25/2023] Open
Abstract
Tau is a Microtubule-associated protein that induces and stabilizes the formation of the Microtubule cytoskeleton and plays an important role in neurodegenerative diseases. The Microtubules binding region of Tau has been determined for a long time but where and how Tau binds to its partner still remain a topic of debate. We used Site Directed Spin Labeling combined with EPR spectroscopy to monitor Tau upon binding to either Taxol-stabilized MTs or to αβ-tubulin when Tau is directly used as an inducer of MTs formation. Using maleimide-functionalized labels grafted on the two natural cysteine residues of Tau, we found in both cases that Tau remains highly flexible in these regions confirming the fuzziness of Tau:MTs complexes. More interestingly, using labels linked by a disulfide bridge, we evidenced for the first time thiol disulfide exchanges between αβ-tubulin or MTs and Tau. Additionally, Tau fragments having the two natural cysteines or variants containing only one of them were used to determine the role of each cysteine individually. The difference observed in the label release kinetics between preformed MTs or Tau-induced MTs, associated to a comparison of structural data, led us to propose two putative binding sites of Tau on αβ-tubulin.
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Affiliation(s)
- Marlène Martinho
- Aix-Marseille Univ, CNRS, UMR 7281 BIP, Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Diane Allegro
- Aix-Marseille Univ, CNRS, UMR 7051, INP, Institut de Neurophysiopathologie, Marseille, France
| | | | - Charlotte Chabaud
- Aix-Marseille Univ, CNRS, UMR 7281 BIP, Bioénergétique et Ingénierie des Protéines, Marseille, France.,Aix-Marseille Univ, CNRS, UMR 7051, INP, Institut de Neurophysiopathologie, Marseille, France
| | - Emilien Etienne
- Aix-Marseille Univ, CNRS, UMR 7281 BIP, Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Hervé Kovacic
- Aix-Marseille Univ, CNRS, UMR 7051, INP, Institut de Neurophysiopathologie, Marseille, France
| | - Bruno Guigliarelli
- Aix-Marseille Univ, CNRS, UMR 7281 BIP, Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Vincent Peyrot
- Aix-Marseille Univ, CNRS, UMR 7051, INP, Institut de Neurophysiopathologie, Marseille, France
| | | | - Valérie Belle
- Aix-Marseille Univ, CNRS, UMR 7281 BIP, Bioénergétique et Ingénierie des Protéines, Marseille, France.
| | - Pascale Barbier
- Aix-Marseille Univ, CNRS, UMR 7051, INP, Institut de Neurophysiopathologie, Marseille, France.
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26
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Cattani J, Subramaniam V, Drescher M. Room-temperature in-cell EPR spectroscopy: alpha-Synuclein disease variants remain intrinsically disordered in the cell. Phys Chem Chem Phys 2018; 19:18147-18151. [PMID: 28696461 DOI: 10.1039/c7cp03432f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human alpha-Synuclein (aS), implicated in Parkinson's disease, adopts a rich variety of different conformations depending on the macromolecular context. In order to unravel its pathophysiological role, monitoring its intracellular conformational state and identifying differences for the disease variants is crucial. Here, we present an intracellular spectroscopy approach based on a systematic spin-labeling site-scan in combination with intracellular electron paramagnetic resonance spectroscopy determining conformations on a molecular scale. A quantitative and model-based data analysis revealed that the vast majority of aS, be it wild-type or disease variants A30P or A53T, exists in the monomeric intrinsically disordered form in the cell.
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Affiliation(s)
- Julia Cattani
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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27
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Biller JR, Barnes R, Han S. Perspective of Overhauser dynamic nuclear polarization for the study of soft materials. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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Kaisersberger Vincek M, Mor A, Gorgieva S, Kokol V. Antibacterial activity and cytotoxycity of gelatine-conjugated lysine-based peptides. J Biomed Mater Res A 2017; 105:3110-3126. [PMID: 28771959 DOI: 10.1002/jbm.a.36164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/28/2017] [Indexed: 12/21/2022]
Abstract
The effect of the coupling approach (chemical by using carbodiimide chemistry, and enzymatic by using transglutaminase) of a hydrophilic ɛ-poly-L-lysine (ɛPL) and a structurally-hydrophobic oligo-acyl-lysyl (OAK) to a gelatine (GEL) macromolecule, and their antibacterial activity against Gram-negative E. coli and Gram-positive S. aureus bacteria, as well as cytotoxicity to human osteoblast cells was studied as potential macromolecules for biomedical applications. Different spectroscopic (ultraviolet-visible, infrared, fluorescence, and electron paramagnetic resonance) and separation (size-exclusion chromatography and capillary zone electrophoresis) techniques, as well as zeta-potential analysis were performed to confirm the ɛPL/OAK covalent coupling and to determine their amount and orientation of the immobilization. The highest and kinetically the fastest reduction of bacteria (≥77% against E. coli vs. ≥82% against S. aureus) was achieved with GEL functionalized with ɛPL/OAK by the chemical grafting-to approach being correlated with conformationally the highly-flexible ˝brush-like˝ orientation linkage of peptides, enable its targeted and rapid interactions with bacteria membrane. The up to 400-fold lower yield of OAKs being immobilized may be related also to its cationic charge and hydrophobic alkyl chain moieties, compared to more hydrophilic ɛPL easily causing random polymerization and self-conjugation. The ɛPL/OAK-functionalized GEL did not induce citotoxicity to osteoblasts, even at ∼25-fold higher concentration than bacterial minimum inhibitory (MIC) concentration of ɛPL/OAK. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3110-3126, 2017.
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Affiliation(s)
- Maja Kaisersberger Vincek
- Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, Maribor, Slovenia
| | - Amram Mor
- Department of Biotechnology & Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Selestina Gorgieva
- Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, Maribor, Slovenia
| | - Vanja Kokol
- Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, Maribor, Slovenia
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29
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Etienne E, Le Breton N, Martinho M, Mileo E, Belle V. SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site-directed spin labeling experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:714-719. [PMID: 28078740 DOI: 10.1002/mrc.4578] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 05/24/2023]
Abstract
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non-expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL-EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL-EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- E Etienne
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - N Le Breton
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
- Queen Mary University of London, School of Biological and Chemical Sciences, UK
| | - M Martinho
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
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30
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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31
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Freeman AJ, Stevens M, Declais AC, Leahy A, Mackay K, El Mkami H, Lilley DMJ, Norman DG. Analysis of the Intrinsically Disordered N-Terminus of the DNA Junction-Resolving Enzyme T7 Endonuclease I: Identification of Structure Formed upon DNA Binding. Biochemistry 2016; 55:4166-72. [PMID: 27387136 PMCID: PMC4990344 DOI: 10.1021/acs.biochem.6b00242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/14/2016] [Indexed: 02/07/2023]
Abstract
The four-way (Holliday) DNA junction of homologous recombination is processed by the symmetrical cleavage of two strands by a nuclease. These junction-resolving enzymes bind to four-way junctions in dimeric form, distorting the structure of the junction in the process. Crystal structures of T7 endonuclease I have been determined as free protein, and the complex with a DNA junction. In neither crystal structure was the N-terminal 16-amino acid peptide visible, yet deletion of this peptide has a marked effect on the resolution process. Here we have investigated the N-terminal peptide by inclusion of spin-label probes at unique sites within this region, studied by electron paramagnetic resonance. Continuous wave experiments show that these labels are mobile in the free protein but become constrained on binding a DNA junction, with the main interaction occurring for residues 7-10 and 12. Distance measurements between equivalent positions within the two peptides of a dimer using PELDOR showed that the intermonomeric distances for residues 2-12 are long and broadly distributed in the free protein but are significantly shortened and become more defined on binding to DNA. These results suggest that the N-terminal peptides become more organized on binding to the DNA junction and nestle into the minor grooves at the branchpoint, consistent with the biochemical data indicating an important role in the resolution process. This study demonstrates the presence of structure within a protein region that cannot be viewed by crystallography.
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Affiliation(s)
- Alasdair
D. J. Freeman
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Michael Stevens
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Anne-Cecile Declais
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Adam Leahy
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Katherine Mackay
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Hassane El Mkami
- School
of Physics and Astronomy, University of
St Andrews, St Andrews FE2 4KM, U.K.
| | - David M. J. Lilley
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - David G. Norman
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
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32
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Song L, Liu Z, Kaur P, Esquiaqui JM, Hunter RI, Hill S, Smith GM, Fanucci GE. Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:188-196. [PMID: 26923151 DOI: 10.1016/j.jmr.2016.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W-(∼94 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.
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Affiliation(s)
- Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Pavanjeet Kaur
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Robert I Hunter
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Graham M Smith
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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33
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Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
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Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
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34
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Jeschke G. Ensemble models of proteins and protein domains based on distance distribution restraints. Proteins 2016; 84:544-60. [PMID: 26994550 DOI: 10.1002/prot.25000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zürich, 8093, Switzerland
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35
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Le Breton N, Adrianaivomananjaona T, Gerbaud G, Etienne E, Bisetto E, Dautant A, Guigliarelli B, Haraux F, Martinho M, Belle V. Dimerization interface and dynamic properties of yeast IF1 revealed by Site-Directed Spin Labeling EPR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:89-97. [PMID: 26518384 DOI: 10.1016/j.bbabio.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 11/21/2022]
Abstract
The mitochondrial ATPase inhibitor, IF1, regulates the activity of the mitochondrial ATP synthase. The oligomeric state of IF1 related to pH is crucial for its inhibitory activity. Although extensive structural studies have been performed to characterize the oligomeric states of bovine IF1, only little is known concerning those of yeast IF1. While bovine IF1 can be found as an inhibitory dimer at low pH and a non-inhibitory tetramer at high pH, a monomer/dimer equilibrium has been described for yeast IF1, high pH values favoring the monomeric state. Combining different strategies involving the grafting of nitroxide spin labels combined with Electron Paramagnetic Resonance (EPR) spectroscopy, the present study brings the first structural characterization, at the residue level, of yeast IF1 in its dimeric form. The results show that the dimerization interface involves the central region of the peptide revealing that the dimer corresponds to a non-inhibitory state. Moreover, we demonstrate that the C-terminal region of the peptide is highly dynamic and that this segment is probably folded back onto the central region. Finally, the pH-dependence of the inter-label distance distribution has been observed indicating a conformational change between two structural states in the dimer.
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Affiliation(s)
- Nolwenn Le Breton
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Tiona Adrianaivomananjaona
- Lifesearch, 72 rue du Fauboug St Honoré, F-75008 Paris, France; CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; CEA, CNRS, Université Paris Sud, Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, F-91191 Gif sur Yvette, France
| | - Guillaume Gerbaud
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Emilien Etienne
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Elena Bisetto
- CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, I-33100 Udine, Italy
| | - Alain Dautant
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, F-33000 Bordeaux, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Francis Haraux
- CEA, Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France; CEA, CNRS, Université Paris Sud, Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, F-91191 Gif sur Yvette, France.
| | - Marlène Martinho
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France
| | - Valérie Belle
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille, France.
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