1
|
Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.01.543259. [PMID: 37333393 PMCID: PMC10274692 DOI: 10.1101/2023.06.01.543259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
Collapse
Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| |
Collapse
|
2
|
Dunleavy KM, Li T, Milshteyn E, Jaufer AM, Walker SA, Fanucci GE. Charge Distribution Patterns of IA 3 Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble. J Phys Chem B 2023; 127:9734-9746. [PMID: 37936402 DOI: 10.1021/acs.jpcb.3c06170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically disordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based on the intrinsically disordered protein (IDP) parameters of fractional net charge (FNC), net charge density per residue (NCPR), and charge patterning (κ), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs, thus making IA3 a bimodal domain IDP. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes, analyzed in terms of their local tumbling volume (VL), provide insights into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution patterns within a conformational subclass can impact bound water hydration dynamics, thus possibly offering an alternative thermodynamic property that can encode conformational binding and behavior of IDPs and liquid-liquid phase separations.
Collapse
Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Shamon A Walker
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| |
Collapse
|
3
|
Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023; 13:biom13010124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late 1990s when a few groups, working independently, convinced the community that these 'weird' proteins could have important functions. Over the past two decades, it has become clear that IDPs play critical roles in a multitude of biological phenomena with prominent examples including coordination in signaling hubs, enabling gene regulation, and regulating ion channels, just to name a few. One contributing factor that delayed appreciation of IDP functional significance is the experimental difficulty in characterizing their dynamic conformations. The combined application of multiple methods, termed integrative structural biology, has emerged as an essential approach to understanding IDP phenomena. Here, we review some of the recent applications of the integrative structural biology philosophy to study IDPs.
Collapse
|
4
|
Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
Collapse
Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| |
Collapse
|
5
|
Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
Collapse
Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| |
Collapse
|
6
|
Bonucci A, Palomino-Schätzlein M, Malo de Molina P, Arbe A, Pierattelli R, Rizzuti B, Iovanna JL, Neira JL. Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1. Front Mol Biosci 2021; 8:684622. [PMID: 34291085 PMCID: PMC8287036 DOI: 10.3389/fmolb.2021.684622] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023] Open
Abstract
The intracellular environment is crowded with macromolecules, including sugars, proteins and nucleic acids. In the cytoplasm, crowding effects are capable of excluding up to 40% of the volume available to any macromolecule when compared to dilute conditions. NUPR1 is an intrinsically disordered protein (IDP) involved in cell-cycle regulation, stress-cell response, apoptosis processes, DNA binding and repair, chromatin remodeling and transcription. Simulations of molecular crowding predict that IDPs can adopt compact states, as well as more extended conformations under crowding conditions. In this work, we analyzed the conformation and dynamics of NUPR1 in the presence of two synthetic polymers, Ficoll-70 and Dextran-40, which mimic crowding effects in the cells, at two different concentrations (50 and 150 mg/ml). The study was carried out by using a multi-spectroscopic approach, including: site-directed spin labelling electron paramagnetic resonance spectroscopy (SDSL-EPR), nuclear magnetic resonance spectroscopy (NMR), circular dichroism (CD), small angle X-ray scattering (SAXS) and dynamic light scattering (DLS). SDSL-EPR spectra of two spin-labelled mutants indicate that there was binding with the crowders and that the local dynamics of the C and N termini of NUPR1 were partially affected by the crowders. However, the overall disordered nature of NUPR1 did not change substantially in the presence of the crowders, as shown by circular dichroism CD and NMR, and further confirmed by EPR. The changes in the dynamics of the paramagnetic probes appear to be related to preferred local conformations and thus crowding agents partially affect some specific regions, further pinpointing that NUPR1 flexibility has a key physiological role in its activity.
Collapse
Affiliation(s)
- Alessio Bonucci
- CERM & Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino (Florence), Italy
| | | | - Paula Malo de Molina
- Centro de Física de Materiales (CFM), CSIC-UPV/EHU, San Sebastián, Spain.,IKERBASQUE-Basque Foundation for Science, Bilbao, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM), CSIC-UPV/EHU, San Sebastián, Spain
| | - Roberta Pierattelli
- CERM & Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino (Florence), Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, Italy.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - José L Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain.,IDIBE, Universidad Miguel Hernández, Elche (Alicante), Spain
| |
Collapse
|
7
|
Torricella F, Pierro A, Mileo E, Belle V, Bonucci A. Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140653. [PMID: 33757896 DOI: 10.1016/j.bbapap.2021.140653] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.
Collapse
Affiliation(s)
- F Torricella
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - A Bonucci
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy; Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France.
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Perez AF, Taing KR, Quon JC, Flores A, Ba Y. Effect of Type I Antifreeze Proteins on the Freezing and Melting Processes of Cryoprotective Solutions Studied by Site-Directed Spin Labeling Technique. CRYSTALS 2019; 9. [PMID: 33224522 PMCID: PMC7678753 DOI: 10.3390/cryst9070352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Antifreeze proteins (AFPs) protect organisms living in subzero environments from freezing injury, which render them potential applications for cryopreservation of living cells, organs, and tissues. Cryoprotective agents (CPAs), such as glycerol and propylene glycol, have been used as ingredients to treat cellular tissues and organs to prevent ice crystal’s formation at low temperatures. To assess AFP’s function in CPA solutions, we have the applied site-directed spin labeling technique to a Type I AFP. A two-step process to prevent bulk freezing of the CPA solutions was observed by the cryo-photo microscopy, i.e., (1) thermodynamic freezing point depression by the CPAs; and (2) inhibition to the growth of seed ice crystals by the AFP. Electron paramagnetic resonance (EPR) experiments were also carried out from room temperature to 97 K, and vice versa. The EPR results indicate that the spin labeled AFP bound to ice surfaces, and inhibit the growths of ice through the bulk freezing processes in the CPA solutions. The ice-surface bound AFP in the frozen matrices could also prevent the formation of large ice crystals during the melting processes of the solutions. Our study illustrates that AFPs can play an active role in CPA solutions for cryopreservation applications.
Collapse
Affiliation(s)
- Adiel F Perez
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Kyle R Taing
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Justin C Quon
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Antonia Flores
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Yong Ba
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| |
Collapse
|
10
|
Vorobiev AK, Bogdanov AV, Yankova TS, Chumakova NA. Spin Probe Determination of Molecular Orientation Distribution and Rotational Mobility in Liquid Crystals: Model-Free Approach. J Phys Chem B 2019; 123:5875-5891. [PMID: 31251620 DOI: 10.1021/acs.jpcb.9b05431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A model-free approach for simulation of EPR spectra of nitroxide spin probes in liquid-crystalline materials was suggested and used to obtain parameters of molecular orientation and rotational mobility. The developed method is based on experimental recording and numerical simulation of the angular dependence of EPR spectra, which is shown to be much more informative in comparison with a single EPR spectrum. Quantitative spectral simulations considering both local orientational ordering and distribution of local directors in the sample were used for discrimination of models of rotational mobility and orientational alignment. The method was applied for detailed quantitative characterization of axial, orthorhombic, and low-symmetry non-orthorhombic molecular orientation distributions. It is shown that the ordinarily used model of rotational diffusion in a mean-field potential is suitable for the description of molecular mobility and orientational ordering only for relatively low sample temperatures and low-mobility probe molecules with large sizes. In cases of high molecular mobility, the more realistic jump mechanism of molecular moves can be approximately described as quasi-librations. For ordered liquid crystals it was found that mostly the order parameters up to rank 12-14 are essential and easily determined. When well-aligned materials are described, the order parameters up to 18th rank or even higher become meaningful. Both molecular and sample biaxiality is analyzed and quantitatively characterized. The local molecular ordering and sample orientational alignment are quantitatively characterized separately.
Collapse
Affiliation(s)
- A Kh Vorobiev
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - A V Bogdanov
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - T S Yankova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - N A Chumakova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| |
Collapse
|
11
|
Hines JP, Dent MR, Stevens DJ, Burstyn JN. Site-directed spin label electron paramagnetic resonance spectroscopy as a probe of conformational dynamics in the Fe(III) "locked-off" state of the CO-sensing transcription factor CooA. Protein Sci 2018; 27:1670-1679. [PMID: 30168206 PMCID: PMC6194275 DOI: 10.1002/pro.3449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 01/30/2023]
Abstract
The transcriptional activator CooA belongs to the CRP/FNR (cAMP receptor protein/fumarate and nitrate reductase) superfamily of transcriptional regulators and uses heme to sense carbon monoxide (CO). Effector-driven allosteric activation is well understood in CRP, a CooA homologue. A structural allosteric activation model for CooA exists which parallels that of CRP; however, the role of protein dynamics, which is crucial in CRP, is not well understood in CooA. We employed site-directed spin labeling electron paramagnetic resonance spectroscopy to probe CooA motions on the μs-ms timescale. We created a series of Cys substitution variants, each with a cysteine residue introduced into a key functional region of the protein: K26C, E60C, F132C, D134C, and S175C. The heme environment and DNA binding affinity of each variant were comparable to those of wild-type CooA, with the exception of F132C, which displayed reduced DNA binding affinity. This observation confirms a previously hypothesized role for Phe132 in transmitting the allosteric CO binding signal. Osmolyte perturbation studies of Fe(III) "locked-off" CooA variants labeled with either MTSL or MAL-6 nitroxide spin labels revealed that multicomponent EPR spectra report on conformational flexibility on the μs-ms timescale. Multiple dynamic populations exist at every site examined in the structurally uncharacterized Fe(III) "locked-off" CooA. This observation suggests that, in direct contrast to effector-free CRP, Fe(III) "locked-off" CooA undergoes conformational exchange on the μs-ms timescale. Importantly, we establish MAL-6 as a spin label with a redox-stable linkage that may be utilized to compare conformational dynamics between functional states of CooA.
Collapse
Affiliation(s)
- Judy P. Hines
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Matthew R. Dent
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Daniel J. Stevens
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Judith N. Burstyn
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| |
Collapse
|
12
|
Flores A, Quon JC, Perez AF, Ba Y. Mechanisms of antifreeze proteins investigated via the site-directed spin labeling technique. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:611-630. [PMID: 29487966 DOI: 10.1007/s00249-018-1285-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/28/2018] [Accepted: 02/15/2018] [Indexed: 12/01/2022]
Abstract
The site-directed spin labeling (SDSL) technique was used to examine the antifreeze mechanisms of type-I antifreeze proteins (AFPs). The effects on the growth of seed ice crystals by the spin-label groups attached to different side chains of the AFPs were observed, and the states of water molecules surrounding the spin-label groups were probed via analyses of variable-temperature (VT) dependent electron paramagnetic resonance (EPR) spectra. The first set of experiments revealed the antifreeze activities of the spin-labeled AFPs at the microscopic level, while the second set of experiments displayed those at the molecular level. The experimental results confirmed the putative ice-binding surface (IBS) of type-I AFPs. The VT EPR spectra indicate that type-I AFPs can inhibit the nucleation of seed ice crystals down to ~ - 20 °C in their aqueous solutions. Thus, the present authors believe that AFPs protect organisms from freezing damage in two ways: (1) inhibiting the nucleation of seed ice crystals, and (2) hindering the growth of seed ice crystals once they have formed. The first mechanism should play a more significant role in protecting against freezing damage among organisms living in cold environments. The VT EPR spectra also revealed that liquid-like water molecules existed around the spin-labeled non-ice-binding side chains of the AFPs frozen within the ice matrices, and ice surrounding the spin-label groups melted at subzero temperatures during the heating process. This manuscript concludes with the proposed model of antifreeze mechanisms of AFPs based on the experimental results.
Collapse
Affiliation(s)
- Antonia Flores
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA
| | - Justin C Quon
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA
| | - Adiel F Perez
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA
| | - Yong Ba
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA.
| |
Collapse
|
13
|
Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018; 57:1366-1370. [DOI: 10.1002/anie.201710184] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| |
Collapse
|
14
|
Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710184] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| |
Collapse
|
15
|
M. Dunleavy K, Milshteyn E, Sorrentino Z, L. Pirman N, Liu Z, B. Chandler M, W. D’Amore P, E. Fanucci G. Spin-label scanning reveals conformational sensitivity of the bound helical interfaces of IA<sub>3</sub>. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
16
|
Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Mateos-Diaz E, Amara S, Roussel A, Longhi S, Cambillau C, Carrière F. Probing Conformational Changes and Interfacial Recognition Site of Lipases With Surfactants and Inhibitors. Methods Enzymol 2017; 583:279-307. [DOI: 10.1016/bs.mie.2016.09.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
19
|
Espinoza-Fonseca LM, Kelekar A. High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2016; 11:1850-6. [PMID: 25855872 DOI: 10.1039/c5mb00170f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
High-resolution characterization of the structure and dynamics of intrinsically disordered proteins (IDPs) remains a challenging task. Consequently, a detailed understanding of the structural and functional features of IDPs remains limited, as very few full-length disordered proteins have been structurally characterized. We have performed microsecond-long molecular dynamics (MD) simulations of Noxa, the smallest member of the large Bcl-2 family of apoptosis regulating proteins, to characterize in atomic-level detail the structural features of a disordered protein. A 2.5 μs MD simulation starting from an unfolded state of the protein revealed the formation of a central antiparallel β-sheet structure flanked by two disordered segments at the N- and C-terminal ends. This topology is in reasonable agreement with protein disorder predictions and available experimental data. We show that this fold plays an essential role in the intracellular function and regulation of Noxa. We demonstrate that unbiased MD simulations in combination with a modern force field reveal structural and functional features of disordered proteins at atomic-level resolution.
Collapse
Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics University of Minnesota, Minneapolis, MN 55455, USA.
| | | |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Georgieva ER, Xiao S, Borbat PP, Freed JH, Eliezer D. Tau binds to lipid membrane surfaces via short amphipathic helices located in its microtubule-binding repeats. Biophys J 2015; 107:1441-52. [PMID: 25229151 DOI: 10.1016/j.bpj.2014.07.046] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/18/2014] [Accepted: 07/24/2014] [Indexed: 11/16/2022] Open
Abstract
Tau is a microtubule-associated protein that is genetically linked to dementia and linked to Alzheimer's disease via its presence in intraneuronal neurofibrillary tangle deposits, where it takes the form of aggregated paired helical and straight filaments. Although the precise mechanisms by which tau contributes to neurodegeneration remain unclear, tau aggregation is commonly considered to be a critical component of tau-mediated pathogenicity. Nevertheless, the context in which tau aggregation begins in vivo is unknown. Tau is enriched in membrane-rich neuronal structures such as axons and growth cones, and can interact with membranes both via intermediary proteins and directly via its microtubule-binding domain (MBD). Membranes efficiently facilitate tau aggregation in vitro, and may therefore provide a physiologically relevant context for nucleating tau aggregation in vivo. Furthermore, tau-membrane interactions may potentially play a role in tau's poorly understood normal physiological functions. Despite the potential importance of direct tau-membrane interactions for tau pathology and physiology, the structural mechanisms that underlie such interactions remain to be elucidated. Here, we employ electron spin resonance spectroscopy to investigate the secondary and long-range structural properties of the MBD of three-repeat tau isoforms when bound to lipid vesicles and membrane mimetics. We show that the membrane interactions of the tau MBD are mediated by short amphipathic helices formed within each of the MBD repeats in the membrane-bound state. To our knowledge, this is the first detailed elucidation of helical tau structure in the context of intact lipid bilayers. We further show, for the first time (to our knowledge), that these individual helical regions behave as independent membrane-binding sites linked by flexible connecting regions. These results represent the first (to our knowledge) detailed structural view of membrane-bound tau and provide insights into potential mechanisms for membrane-mediated tau aggregation. Furthermore, the results may have implications for the structural basis of tau-microtubule interactions and microtubule-mediated tau aggregation.
Collapse
Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York
| | - Shifeng Xiao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Program in Structural Biology, Weill Cornell Medical College, New York, New York
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York.
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Program in Structural Biology, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
22
|
Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. Intrazelluläre NMR- und EPR-Spektroskopie von biologischen Makromolekülen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311320] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
23
|
Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. In-cell NMR and EPR spectroscopy of biomacromolecules. Angew Chem Int Ed Engl 2014; 53:10300-14. [PMID: 25070284 DOI: 10.1002/anie.201311320] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 12/21/2022]
Abstract
The dream of cell biologists is to be able to watch biological macromolecules perform their duties in the intracellular environment of live cells. Ideally, the observation of both the location and the conformation of these macromolecules with biophysical techniques is desired. The development of many fluorescence techniques, including superresolution fluorescence microscopy, has significantly enhanced our ability to spot proteins and other molecules in the crowded cellular environment. However, the observation of their structure and conformational changes while they attend their business is still very challenging. In principle, NMR and EPR spectroscopy can be used to investigate the conformation and dynamics of biological macromolecules in living cells. The development of in-cell magnetic resonance techniques has demonstrated the feasibility of this approach. Herein we review the different techniques with a focus on liquid-state in-cell NMR spectroscopy, provide an overview of applications, and discuss the challenges that lie ahead.
Collapse
Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt (Germany)
| | | | | | | | | |
Collapse
|
24
|
Mileo E, Lorenzi M, Erales J, Lignon S, Puppo C, Le Breton N, Etienne E, Marque SRA, Guigliarelli B, Gontero B, Belle V. Dynamics of the intrinsically disordered protein CP12 in its association with GAPDH in the green alga Chlamydomonas reinhardtii: a fuzzy complex. MOLECULAR BIOSYSTEMS 2014; 9:2869-76. [PMID: 24056937 DOI: 10.1039/c3mb70190e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CP12 is a widespread regulatory protein of oxygenic photosynthetic organisms that contributes to the regulation of the Calvin cycle by forming a supra-molecular complex with at least two enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). CP12 shares some similarities with intrinsically disordered proteins (IDPs) depending on its redox state. In this study, site-directed spin labeling (SDSL) combined with EPR spectroscopy was used to probe the dynamic behavior of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH, the first step towards ternary complex formation. The two N-terminal cysteine residues were labeled using the classical approach while the tyrosine located at the C-terminal end of CP12 was modified following an original procedure. The results show that the label grafted at the C-terminal extremity is in the vicinity of the interaction site whereas the N-terminal region remains fully disordered upon binding to GAPDH. In conclusion, GAPDH-CP12 is a fuzzy complex, in which the N-terminal region of CP12 keeps a conformational freedom in the bound form. This fuzziness could be one of the keys to facilitate binding of PRK to CP12-GAPDH and to form the ternary supra-molecular complex.
Collapse
Affiliation(s)
- Elisabetta Mileo
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Breton NL, Martinho M, Kabytaev K, Topin J, Mileo E, Blocquel D, Habchi J, Longhi S, Rockenbauer A, Golebiowski J, Guigliarelli B, Marque SRA, Belle V. Diversification of EPR signatures in site directed spin labeling using a β-phosphorylated nitroxide. Phys Chem Chem Phys 2014; 16:4202-9. [DOI: 10.1039/c3cp54816c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
26
|
Mileo E, Etienne E, Martinho M, Lebrun R, Roubaud V, Tordo P, Gontero B, Guigliarelli B, Marque SRA, Belle V. Enlarging the Panoply of Site-Directed Spin Labeling Electron Paramagnetic Resonance (SDSL-EPR): Sensitive and Selective Spin-Labeling of Tyrosine Using an Isoindoline-Based Nitroxide. Bioconjug Chem 2013; 24:1110-7. [DOI: 10.1021/bc4000542] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisabetta Mileo
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| | - Emilien Etienne
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| | - Marlène Martinho
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| | - Régine Lebrun
- Aix-Marseille Université, Plate-forme Protéomique
IMM, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Valérie Roubaud
- Aix-Marseille Université, CNRS, ICR UMR 7273, Avenue Escadrille
Normandie-Niemen, 13397 Marseille Cedex 20, France
| | - Paul Tordo
- Aix-Marseille Université, CNRS, ICR UMR 7273, Avenue Escadrille
Normandie-Niemen, 13397 Marseille Cedex 20, France
| | - Brigitte Gontero
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| | - Sylvain R. A. Marque
- Aix-Marseille Université, CNRS, ICR UMR 7273, Avenue Escadrille
Normandie-Niemen, 13397 Marseille Cedex 20, France
| | - Valérie Belle
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex
20, France
| |
Collapse
|
27
|
Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25496. [PMID: 28516015 PMCID: PMC5424799 DOI: 10.4161/idp.25496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/13/2023]
Abstract
The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for “intrinsically disordered protein OR natively unfolded protein” returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a “Digested Disorder” project, which will encompass a series of reader’s digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicince; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| |
Collapse
|
28
|
Lorenzi M, Sylvi L, Gerbaud G, Mileo E, Halgand F, Walburger A, Vezin H, Belle V, Guigliarelli B, Magalon A. Conformational selection underlies recognition of a molybdoenzyme by its dedicated chaperone. PLoS One 2012. [PMID: 23185350 PMCID: PMC3501500 DOI: 10.1371/journal.pone.0049523] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Molecular recognition is central to all biological processes. Understanding the key role played by dedicated chaperones in metalloprotein folding and assembly requires the knowledge of their conformational ensembles. In this study, the NarJ chaperone dedicated to the assembly of the membrane-bound respiratory nitrate reductase complex NarGHI, a molybdenum-iron containing metalloprotein, was taken as a model of dedicated chaperone. The combination of two techniques ie site-directed spin labeling followed by EPR spectroscopy and ion mobility mass spectrometry, was used to get information about the structure and conformational dynamics of the NarJ chaperone upon binding the N-terminus of the NarG metalloprotein partner. By the study of singly spin-labeled proteins, the E119 residue present in a conserved elongated hydrophobic groove of NarJ was shown to be part of the interaction site. Moreover, doubly spin-labeled proteins studied by pulsed double electron-electron resonance (DEER) spectroscopy revealed a large and composite distribution of inter-label distances that evolves into a single preexisting one upon complex formation. Additionally, ion mobility mass spectrometry experiments fully support these findings by revealing the existence of several conformers in equilibrium through the distinction of different drift time curves and the selection of one of them upon complex formation. Taken together our work provides a detailed view of the structural flexibility of a dedicated chaperone and suggests that the exquisite recognition and binding of the N-terminus of the metalloprotein is governed by a conformational selection mechanism.
Collapse
Affiliation(s)
- Magali Lorenzi
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Léa Sylvi
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Guillaume Gerbaud
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Elisabetta Mileo
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Frédéric Halgand
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Anne Walburger
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Hervé Vezin
- Laboratoire de Spectrochimie Infrarouge et Raman (UMR8516), Villeneuve d'Ascq, France
| | - Valérie Belle
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
| |
Collapse
|
29
|
Woodham AW, Da Silva DM, Skeate JG, Raff AB, Ambroso MR, Brand HE, Isas JM, Langen R, Kast WM. The S100A10 subunit of the annexin A2 heterotetramer facilitates L2-mediated human papillomavirus infection. PLoS One 2012; 7:e43519. [PMID: 22927980 PMCID: PMC3425544 DOI: 10.1371/journal.pone.0043519] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 07/23/2012] [Indexed: 12/13/2022] Open
Abstract
Mucosotropic, high-risk human papillomaviruses (HPV) are sexually transmitted viruses that are causally associated with the development of cervical cancer. The most common high-risk genotype, HPV16, is an obligatory intracellular virus that must gain entry into host epithelial cells and deliver its double stranded DNA to the nucleus. HPV capsid proteins play a vital role in these steps. Despite the critical nature of these capsid protein-host cell interactions, the precise cellular components necessary for HPV16 infection of epithelial cells remains unknown. Several neutralizing epitopes have been identified for the HPV16 L2 minor capsid protein that can inhibit infection after initial attachment of the virus to the cell surface, which suggests an L2-specific secondary receptor or cofactor is required for infection, but so far no specific L2-receptor has been identified. Here, we demonstrate that the annexin A2 heterotetramer (A2t) contributes to HPV16 infection and co-immunoprecipitates with HPV16 particles on the surface of epithelial cells in an L2-dependent manner. Inhibiting A2t with an endogenous annexin A2 ligand, secretory leukocyte protease inhibitor (SLPI), or with an annexin A2 antibody significantly reduces HPV16 infection. With electron paramagnetic resonance, we demonstrate that a previously identified neutralizing epitope of L2 (aa 108-120) specifically interacts with the S100A10 subunit of A2t. Additionally, mutation of this L2 region significantly reduces binding to A2t and HPV16 pseudovirus infection. Furthermore, downregulation of A2t with shRNA significantly decreases capsid internalization and infection by HPV16. Taken together, these findings indicate that A2t contributes to HPV16 internalization and infection of epithelial cells and this interaction is dependent on the presence of the L2 minor capsid protein.
Collapse
Affiliation(s)
- Andrew W. Woodham
- Departments of Molecular Microbiology & Immunology, University of Southern California, Los Angeles, California, United States of America
| | - Diane M. Da Silva
- Department of Obstetrics & Gynecology, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Joseph G. Skeate
- Departments of Molecular Microbiology & Immunology, University of Southern California, Los Angeles, California, United States of America
| | - Adam B. Raff
- Departments of Molecular Microbiology & Immunology, University of Southern California, Los Angeles, California, United States of America
| | - Mark R. Ambroso
- Department of Biochemistry & Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Heike E. Brand
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - J. Mario Isas
- Department of Biochemistry & Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ralf Langen
- Department of Biochemistry & Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - W. Martin Kast
- Departments of Molecular Microbiology & Immunology, University of Southern California, Los Angeles, California, United States of America
- Department of Obstetrics & Gynecology, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| |
Collapse
|
30
|
Höbartner C, Sicoli G, Wachowius F, Gophane DB, Sigurdsson ST. Synthesis and Characterization of RNA Containing a Rigid and Nonperturbing Cytidine-Derived Spin Label. J Org Chem 2012; 77:7749-54. [DOI: 10.1021/jo301227w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
31
|
Martinho M, Habchi J, El Habre Z, Nesme L, Guigliarelli B, Belle V, Longhi S. Assessing induced folding within the intrinsically disordered C-terminal domain of the Henipavirus nucleoproteins by site-directed spin labeling EPR spectroscopy. J Biomol Struct Dyn 2012; 31:453-71. [PMID: 22881220 DOI: 10.1080/07391102.2012.706068] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This work aims at characterizing structural transitions within the intrinsically disordered C-terminal domain of the nucleoprotein (NTAIL) from the Nipah and Hendra viruses, two recently emerged pathogens gathered within the Henipavirus genus. To this end, we used site-directed spin labeling combined with electron paramagnetic resonance spectroscopy to investigate the α-helical-induced folding that Henipavirus NTAIL domains undergo in the presence of the C-terminal X domain of the phosphoprotein (PXD). For each NTAIL protein, six positions located within four previously proposed molecular recognition elements (MoREs) were targeted for spin labeling, with three of these positions (475, 481, and 487) falling within the MoRE responsible for binding to PXD (Box3). A detailed analysis of the impact of the partner protein on the labeled NTAIL variants revealed a dramatic modification in the environment of the spin labels grafted within Box3, with the observed modifications supporting the formation of an induced α-helix within this region. In the free state, the slightly lower mobility of the spin labels grafted within Box3 as compared to the other positions suggests the existence of a transiently populated α-helix, as already reported for measles virus (MeV) NTAIL. Comparison with the well-characterized MeV NTAIL-PXD system, allowed us to validate the structural models of Henipavirus NTAIL-PXD complexes that we previously proposed. In addition, this study highlighted a few notable differences between the Nipah and Hendra viruses. In particular, the observation of composite spectra for the free form of the Nipah virus NTAIL variants spin labeled in Box3 supports conformational heterogeneity of this partly pre-configured α-helix, with the pre-existence of stable α-helical segments. Altogether these results provide insights into the molecular mechanisms of the Henipavirus NTAIL-PXD binding reaction.
Collapse
Affiliation(s)
- Marlène Martinho
- CNRS, Aix Marseille Université, IMM FR 3479, BIP UMR 7281, 13402 Marseille, France
| | | | | | | | | | | | | |
Collapse
|
32
|
Habchi J, Martinho M, Gruet A, Guigliarelli B, Longhi S, Belle V. Monitoring structural transitions in IDPs by site-directed spin labeling EPR spectroscopy. Methods Mol Biol 2012; 895:361-386. [PMID: 22760328 DOI: 10.1007/978-1-61779-927-3_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a technique that specifically detects unpaired electrons. EPR sensitive reporter groups (spin labels or spin probes) can be introduced into biological systems via site-directed spin labeling (SDSL). This is usually accomplished by cysteine-substitution mutagenesis followed by covalent modification of the unique sulfhydryl group with a selective nitroxide reagent. SDSL EPR spectroscopy has been shown to be a sensitive and powerful method to study structural transitions within intrinsically disordered proteins (IDPs). In this chapter, we provide a detailed experimental protocol for this approach and present a few examples of EPR spectral shapes illustrative of various mobility regimes of the spin probe, reflecting different protein topologies.
Collapse
Affiliation(s)
- Johnny Habchi
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS and Aix-Marseille Université, Marseille, France
| | | | | | | | | | | |
Collapse
|
33
|
Carlotto S, Zerbetto M, Shabestari MH, Moretto A, Formaggio F, Crisma M, Toniolo C, Huber M, Polimeno A. In silico interpretation of cw-ESR at 9 and 95 GHz of mono- and bis- TOAC-labeled Aib-homopeptides in fluid and frozen acetonitrile. J Phys Chem B 2011; 115:13026-36. [PMID: 21970372 DOI: 10.1021/jp2063645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we address the interpretation of molecular properties of selected singly and doubly spin-labeled peptides from continuous-wave electron spin resonance (cw-ESR) spectroscopy. This study is performed by means of an integrated computational approach that merges a stochastic treatment of long-term dynamics to ad hoc methodologies for the calculation of structural properties. In particular, our method is based on (i) the determination of geometric and local magnetic parameters of the peptides by quantum mechanical density functional calculations by taking into account solvent contribution; (ii) the hydrodynamic evaluation of dissipative properties; and (iii) molecular dynamics including equilibrium distribution of molecular conformations. The system is then described by a stochastic Liouville equation in which the spin Hamiltonian for the two electron spins, interacting with each other and coupled to two (14)N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow coordinates. cw-ESR spectra are simulated for selected peptides built from the non-natural α-aminoacids α-aminoisobutyric acid (Aib) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, we study the -Aib-TOAC-Aib- singly labeled tripeptide and the -Aib-TOAC-(Aib)(7)- singly labeled and -Aib-TOAC-(Aib)(5)-TOAC-Aib- doubly labeled nonapeptides. We show that good agreement is obtained with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling is a powerful approach to the investigation of both molecular dynamics and 3D-structural properties.
Collapse
Affiliation(s)
- Silvia Carlotto
- Department of Chemistry, University of Padova, Padova, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|