1
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Saade C, Pozza A, Bonneté F, Finet S, Lutz-Bueno V, Tully MD, Varela PF, Lacapère JJ, Combet S. Enhanced structure/function of mTSPO translocator in lipid:surfactant mixed micelles. Biochimie 2024; 224:3-15. [PMID: 38663457 DOI: 10.1016/j.biochi.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/06/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
TSPO is a ubiquitous transmembrane protein used as a pharmacological marker in neuroimaging. The only known atomic structure of mammalian TSPOs comes from the solution NMR of mouse TSPO (mTSPO) bound to the PK11195 ligand and in a DPC surfactant environment. No structure is available in a biomimetic environment and without PK11195 which strongly stiffens the protein. We measured the effect of different amphiphilic environments on ligand-free mTSPO to study its structure/function and find optimal solubilization conditions. By replacing the SDS surfactant, where the recombinant protein is purified, with mixed lipid:surfactant (DMPC:DPC) micelles at different ratios (0:1, 1:2, and 2:1, w:w), the α-helix content and interactions and the intrinsic tryptophan (Trp) fluorescence of mTSPO are gradually increased. Small-angle X-ray scattering (SAXS) shows a more extended mTSPO/belt complex with the addition of lipids: Dmax ∼95 Å in DPC alone versus ∼142 Å in DMPC:DPC (1:2). SEC-MALLS shows that the molecular composition of the mTSPO belt is ∼98 molecules for DPC alone and ∼58 DMPC and ∼175 DPC for DMPC:DPC (1:2). Additionally, DMPC:DPC micelles stabilize mTSPO compared to DPC alone, where the protein has a greater propensity to aggregate. These structural changes are consistent with the increased affinity of mTSPO for the PK11195 ligand in presence of lipids (Kd ∼70 μM in DPC alone versus ∼0.91 μM in DMPC:DPC, 1:2), as measured by microscale thermophoresis (MST). In conclusion, mixed lipid:surfactant micelles open new possibilities for the stabilization of membrane proteins and for their study in solution in a more biomimetic amphiphilic environment.
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Affiliation(s)
- Christelle Saade
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France
| | - Alexandre Pozza
- Université Paris Cité, CNRS UMR7099, Biochimie des Protéines Membranaires, F-75005, Paris, France
| | - Françoise Bonneté
- Université Paris Cité, CNRS UMR7099, Biochimie des Protéines Membranaires, F-75005, Paris, France
| | - Stéphanie Finet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université Université, MNHN, IRD, F-75005, Paris, France
| | - Viviane Lutz-Bueno
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France; Paul Scherrer Institut (PSI), Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Mark D Tully
- The European Synchrotron (ESRF), 71 Avenue des Martyrs, F-38043, Grenoble, France
| | - Paloma F Varela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France.
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Napieraj M, Lutton E, Perez J, Boué F, Brûlet A. Destructuration of Canola Protein Gels during In Situ Gastrointestinal Digestion Studied by X-ray Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16226-16238. [PMID: 39041952 DOI: 10.1021/acs.langmuir.4c01341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We are studying the destructuration of canola protein gels, as a solid food model, during in situ gastrointestinal digestion using synchrotron small-angle X-ray scattering (SAXS). Digestion of two gels, prepared by heating pH 8 and pH 11 solutions, was carried out by diffusion of enzymatic juices into the gel from the top of the capillary and monitored for several tens of hours. Very similar time evolutions of SAXS curves occur at different positions of the gel in the capillary, with a delay determined by the distance from the surface initially in contact with the digestive juice. The main phenomena observed are (i) at the scale of the protein conformation (1-5 nm). The scattering curve is a power law, the exponent of which measures the compactness (related to the degree of unfolding). It can be plotted as a function of the characteristic size of proteins/and interprotein distances and as a function of the scattering intensity. Such diagrams clearly show successive digestion processes. For the pH 11 gel, in which proteins are initially hardly unfolded, the digestive processes are unfolding (1st step), recompaction-aggregation phenomena (2nd step) due to gastrointestinal pH conditions and enzymatic cleavage, further unfolding-disaggregation (3rd step), and final protein cleavage (4th step) down to small peptides. For the pH 8 gel, proteins are initially unfolded, and only the last three steps are observed, showing the influence of easier access for the enzymes. (ii) At the scale of large aggregates (10-50 nm), we observe for both gels a decrease in the size and/or number of these aggregates during digestion and alteration of their interfaces. (iii) At the scale of the secondary protein structure, wide-angle X-ray scattering is very useful for detecting the degradation of the secondary protein structure at different steps of digestion.
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Affiliation(s)
- Maja Napieraj
- Laboratoire Léon Brillouin, UMR12 CEA-CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif sur Yvette, France
| | - Evelyne Lutton
- Mathématiques et Informatique Appliquée─Paris, UMR518 AgroParisTech-INRAE, Université Paris-Saclay, 91120 Palaiseau, France
- Institut des Systèmes Complexes, 75013 Paris, France
| | - Javier Perez
- SWING, Synchrotron SOLEIL, Saint-Aubin - BP 48, 91192 Gif sur Yvette, France
| | - François Boué
- Laboratoire Léon Brillouin, UMR12 CEA-CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif sur Yvette, France
| | - Annie Brûlet
- Laboratoire Léon Brillouin, UMR12 CEA-CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif sur Yvette, France
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3
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Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [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: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
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4
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Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023; 34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [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: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Oulu, Finland
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5
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. J Phys Chem B 2023; 127:4746-4760. [PMID: 37200094 PMCID: PMC10875986 DOI: 10.1021/acs.jpcb.3c01619] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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6
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.531990. [PMID: 36993592 PMCID: PMC10054940 DOI: 10.1101/2023.03.12.531990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory Random Coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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7
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Effects of addition of styrene-co-methacrylate ionomers neutralized with various monovalent cations on asphaltene dispersion in heavy oil. Macromol Res 2023. [DOI: 10.1007/s13233-023-00122-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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8
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Tashiro D, Suetaka S, Sato N, Ooka K, Kunihara T, Kudo H, Inatomi J, Hayashi Y, Arai M. Intron-Encoded Domain of Herstatin, An Autoinhibitor of Human Epidermal Growth Factor Receptors, Is Intrinsically Disordered. Front Mol Biosci 2022; 9:862910. [PMID: 35573740 PMCID: PMC9100580 DOI: 10.3389/fmolb.2022.862910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Human epidermal growth factor receptors (HER/ERBB) form dimers that promote cell proliferation, migration, and differentiation, but overexpression of HER proteins results in cancer. Consequently, inhibitors of HER dimerization may function as effective antitumor drugs. An alternatively spliced variant of HER2, called herstatin, is an autoinhibitor of HER proteins, and the intron 8-encoded 79-residue domain of herstatin, called Int8, binds HER family receptors even in isolation. However, the structure of Int8 remains poorly understood. Here, we revealed by circular dichroism, NMR, small-angle X-ray scattering, and structure prediction that isolated Int8 is largely disordered but has a residual helical structure. The radius of gyration of Int8 was almost the same as that of fully unfolded states, although the conformational ensemble of Int8 was less flexible than random coils. These results demonstrate that Int8 is intrinsically disordered. Thus, Int8 is an interesting example of an intrinsically disordered region with tumor-suppressive activity encoded by an intron. Furthermore, we show that the R371I mutant of Int8, which is defective in binding to HER2, is prone to aggregation, providing a rationale for the loss of function.
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Affiliation(s)
- Daisuke Tashiro
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kunihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Junichi Inatomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- *Correspondence: Munehito Arai,
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9
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Narvekar A, Gawali SL, Hassan PA, Jain R, Dandekar P. pH dependent aggregation and conformation changes of rituximab using SAXS and its comparison with the standard regulatory approach of biophysical characterization. Int J Biol Macromol 2020; 164:3084-3097. [PMID: 32835797 DOI: 10.1016/j.ijbiomac.2020.08.148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
Development of biologics and biosimilars involves extensive physical and structural characterization, which underlines the further course of its implementation. These characterization techniques require considerable standardization and are labor intensive. It is therefore, important to have an immediate, independent and affordable characterization strategy that may meet the regulatory guidelines. In this study, we have compared the standard biophysical characterization of an anti-CD 20 antibody with characterization by small angle x ray scattering (SAXS). Aggregation of this mAb was analyzed using standard techniques like size exclusion HPLC, dynamic light scattering and sedimentation velocity - analytical ultracentrifugation, whereas structure analysis was conducted using mass spectrometry, circular dichroism spectroscopy and fluorescence spectroscopy. Our results demonstrated that the inferences about the state of mAb aggregation and its structure deduced using the standard approaches were comparable to the data interpreted using SAXS. The radius of gyration and the P(r) distribution plot obtained using the SAXS scattering data allowed analysis of aggregation and conformation of mAb via a single experiment. Thus, SAXS can be used as an independent technique to complement orthogonal analysis for determining the aggregation profile and structure of mAbs.
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Affiliation(s)
- Aditya Narvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Santosh L Gawali
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Puthusserickal A Hassan
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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10
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Minić S, Annighöfer B, Hélary A, Hamdane D, Hui Bon Hoa G, Loupiac C, Brûlet A, Combet S. Effect of Ligands on HP-Induced Unfolding and Oligomerization of β-Lactoglobulin. Biophys J 2020; 119:2262-2274. [PMID: 33129832 DOI: 10.1016/j.bpj.2020.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/25/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022] Open
Abstract
To probe intermediate states during unfolding and oligomerization of proteins remains a major challenge. High pressure (HP) is a powerful tool for studying these problems, revealing subtle structural changes in proteins not accessible by other means of denaturation. Bovine β-lactoglobulin (BLG), the main whey protein, has a strong propensity to bind various bioactive molecules such as retinol and resveratrol, two ligands with different affinity and binding sites. By combining in situ HP-small-angle neutron scattering (SANS) and HP-ultraviolet/visible absorption spectroscopy, we report the specific effects of these ligands on three-dimensional conformational and local changes in BLG induced by HP. Depending on BLG concentration, two different unfolding mechanisms are observed in situ under pressures up to ∼300 MPa: either a complete protein unfolding, from native dimers to Gaussian chains, or a partial unfolding with oligomerization in tetramers mediated by disulfide bridges. Retinol, which has a high affinity for the BLG hydrophobic cavity, significantly stabilizes BLG both in three-dimensional and local environments by shifting the onset of protein unfolding by ∼100 MPa. Increasing temperature from 30 to 37°C enhances the hydrophobic stabilization effects of retinol. In contrast, resveratrol, which has a low binding affinity for site(s) on the surface of the BLG, does not induce any significant effect on the structural changes of BLG due to pressure. HP treatment back and forth up to ∼300 MPa causes irreversible covalent oligomerization of BLG. Ab initio modeling of SANS shows that the oligomers formed from the BLG-retinol complex are smaller and more elongated compared to BLG without ligand or in the presence of resveratrol. By combining HP-SANS and HP-ultraviolet/visible absorption spectroscopy, our strategy highlights the crucial role of BLG hydrophobic cavity and opens up new possibilities for the structural determination of HP-induced protein folding intermediates and irreversible oligomerization.
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Affiliation(s)
- Simeon Minić
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR12 CEA-CNRS, CEA-Saclay, Gif-sur-Yvette CEDEX, France.
| | - Burkhard Annighöfer
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR12 CEA-CNRS, CEA-Saclay, Gif-sur-Yvette CEDEX, France
| | - Arnaud Hélary
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR12 CEA-CNRS, CEA-Saclay, Gif-sur-Yvette CEDEX, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Paris CEDEX 05, France
| | - Gaston Hui Bon Hoa
- National Institute of Health and Medical Research (INSERM), Paris, France
| | - Camille Loupiac
- Université de Bourgogne Franche-Comté, AgroSup Dijon, UMRA 02.102 Procédés Alimentaires et Microbiologiques, Equipe Physico-Chimie des Aliments et du Vin, Dijon, France
| | - Annie Brûlet
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR12 CEA-CNRS, CEA-Saclay, Gif-sur-Yvette CEDEX, France
| | - Sophie Combet
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR12 CEA-CNRS, CEA-Saclay, Gif-sur-Yvette CEDEX, France.
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11
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Kouloulia S, Hallin EI, Simbriger K, Amorim IS, Lach G, Amvrosiadis T, Chalkiadaki K, Kampaite A, Truong VT, Hooshmandi M, Jafarnejad SM, Skehel P, Kursula P, Khoutorsky A, Gkogkas CG. Raptor-Mediated Proteasomal Degradation of Deamidated 4E-BP2 Regulates Postnatal Neuronal Translation and NF-κB Activity. Cell Rep 2020; 29:3620-3635.e7. [PMID: 31825840 PMCID: PMC6915327 DOI: 10.1016/j.celrep.2019.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/06/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
The translation initiation repressor 4E-BP2 is deamidated in the brain on asparagines N99/N102 during early postnatal brain development. This post-translational modification enhances 4E-BP2 association with Raptor, a central component of mTORC1 and alters the kinetics of excitatory synaptic transmission. We show that 4E-BP2 deamidation is neuron specific, occurs in the human brain, and changes 4E-BP2 subcellular localization, but not its disordered structure state. We demonstrate that deamidated 4E-BP2 is ubiquitinated more and degrades faster than the unmodified protein. We find that enhanced deamidated 4E-BP2 degradation is dependent on Raptor binding, concomitant with increased association with a Raptor-CUL4B E3 ubiquitin ligase complex. Deamidated 4E-BP2 stability is promoted by inhibiting mTORC1 or glutamate receptors. We further demonstrate that deamidated 4E-BP2 regulates the translation of a distinct pool of mRNAs linked to cerebral development, mitochondria, and NF-κB activity, and thus may be crucial for postnatal brain development in neurodevelopmental disorders, such as ASD. Deamidated 4E-BP2 occurs in neurons and is susceptible to ubiquitination/degradation mTORC1 or glutamate receptor inhibition stabilizes deamidated 4E-BP2 A Raptor-CUL4B ubiquitin ligase complex binds to deamidated 4E-BP2 Deamidated 4E-BP2 regulates postnatal brain translation and NF-κB activity
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Affiliation(s)
- Stella Kouloulia
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Bergen N-5020, Norway
| | - Konstanze Simbriger
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Inês S Amorim
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Gilliard Lach
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Theoklitos Amvrosiadis
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Kleanthi Chalkiadaki
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Agniete Kampaite
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Vinh Tai Truong
- Department of Anesthesia and Alan Edwards Centre for Research on Pain, McGill University, Montréal H3A 0G1, QC, Canada
| | - Mehdi Hooshmandi
- Department of Anesthesia and Alan Edwards Centre for Research on Pain, McGill University, Montréal H3A 0G1, QC, Canada
| | - Seyed Mehdi Jafarnejad
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast BT9 7AE, UK
| | - Paul Skehel
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen N-5020, Norway; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Arkady Khoutorsky
- Department of Anesthesia and Alan Edwards Centre for Research on Pain, McGill University, Montréal H3A 0G1, QC, Canada.
| | - Christos G Gkogkas
- Centre for Discovery Brain Sciences and Patrick Wild Centre, University of Edinburgh, Edinburgh EH8 9XD, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK.
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12
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Abstract
There is a great interest within the research community to understand the structure-function relationship for intrinsically disordered proteins (IDPs); however, the heterogeneous distribution of conformations that IDPs can adopt limits the applicability of conventional structural biology methods. Here, scattering techniques, such as small-angle X-ray scattering, can contribute. In this chapter, we will describe how to make a model-free determination of the radius of gyration by using two different approaches, the Guinier analysis and the pair distance distribution function. The ATSAS package (Franke et al., J Appl Crystallogr 50:1212-1225, 2017) has been used for the evaluation, and throughout the chapter, different examples will be given to illustrate the discussed phenomena, as well as the pros and cons of using the different approaches.
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13
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Raasakka A, Linxweiler H, Brophy PJ, Sherman DL, Kursula P. Direct Binding of the Flexible C-Terminal Segment of Periaxin to β4 Integrin Suggests a Molecular Basis for CMT4F. Front Mol Neurosci 2019; 12:84. [PMID: 31024253 PMCID: PMC6465933 DOI: 10.3389/fnmol.2019.00084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Abstract
The process of myelination in the nervous system requires a coordinated formation of both transient and stable supramolecular complexes. Myelin-specific proteins play key roles in these assemblies, which may link membranes to each other or connect the myelinating cell cytoskeleton to the extracellular matrix. The myelin protein periaxin is known to play an important role in linking the Schwann cell cytoskeleton to the basal lamina through membrane receptors, such as the dystroglycan complex. Mutations that truncate periaxin from the C terminus cause demyelinating peripheral neuropathy, Charcot-Marie-Tooth (CMT) disease type 4F, indicating a function for the periaxin C-terminal region in myelination. We identified the cytoplasmic domain of β4 integrin as a specific high-affinity binding partner for periaxin. The C-terminal region of periaxin remains unfolded and flexible when bound to the third fibronectin type III domain of β4 integrin. Our data suggest that periaxin is able to link the Schwann cell cytoplasm to the basal lamina through a two-pronged interaction via different membrane protein complexes, which bind close to the N and C terminus of this elongated, flexible molecule.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Peter J. Brophy
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Diane L. Sherman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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14
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Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding. Biophys J 2019. [PMID: 29539394 DOI: 10.1016/j.bpj.2018.01.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering. As crowder concentrations increased, the mean radius of gyration of FlgM first decreased but then exhibited an uptick. Ensemble optimization modeling indicated that FlgM conformations under protein crowding segregated into two distinct populations, one compacted and one extended. Coarse-grained simulations showed that compacted conformers fit into an interstitial void and occasionally bind to a surrounding crowder, whereas extended conformers snake through interstitial crevices and bind multiple crowders simultaneously. Crowder-induced conformational segregation may facilitate various cellular functions of IDPs.
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15
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Ameseder F, Radulescu A, Holderer O, Falus P, Richter D, Stadler AM. Relevance of Internal Friction and Structural Constraints for the Dynamics of Denatured Bovine Serum Albumin. J Phys Chem Lett 2018; 9:2469-2473. [PMID: 29688725 DOI: 10.1021/acs.jpclett.8b00825] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A general property of disordered proteins is their structural expansion that results in a high molecular flexibility. The structure and dynamics of bovine serum albumin (BSA) denatured by guanidinium hydrochloride (GndCl) were investigated using small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE). SANS experiments demonstrated the relevance of intrachain interactions for structural expansion. Using NSE experiments, we observed a high internal flexibility of denatured BSA in addition to center-of-mass diffusion detected by dynamic light scattering. Internal motions measured by NSE were described using concepts based on polymer theory. The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). Disulfide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes.
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Affiliation(s)
- Felix Ameseder
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52056 Aachen , Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS) at MLZ, Forschungszentrum Jülich GmbH , 85747 Garching , Germany
| | - Olaf Holderer
- Jülich Centre for Neutron Science (JCNS) at MLZ, Forschungszentrum Jülich GmbH , 85747 Garching , Germany
| | - Peter Falus
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156 , 38042 Grenoble Cedex 9 , France
| | - Dieter Richter
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Andreas M Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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16
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Zheng W, Best RB. An Extended Guinier Analysis for Intrinsically Disordered Proteins. J Mol Biol 2018; 430:2540-2553. [PMID: 29571687 DOI: 10.1016/j.jmb.2018.03.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 12/25/2022]
Abstract
Guinier analysis allows model-free determination of the radius of gyration (Rg) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred Rg within ∼3% of the true Rg. The method is straightforward to implement and extends the range of validity to a maximum qRg of ∼2 versus ∼1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to Rg, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.
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Affiliation(s)
- Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA.
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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17
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Ameseder F, Radulescu A, Khaneft M, Lohstroh W, Stadler AM. Homogeneous and heterogeneous dynamics in native and denatured bovine serum albumin. Phys Chem Chem Phys 2018; 20:5128-5139. [DOI: 10.1039/c7cp08292d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Quasielastic incoherent neutron spectroscopy experiments reveal that chemical denaturation significantly modifies the internal dynamics of bovine serum albumin.
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Affiliation(s)
- Felix Ameseder
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS
- Forschungszentrum Jülich GmbH
- 52425 Jülich
- Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science JCNS
- Forschungszentrum Jülich GmbH, Outstation at MLZ
- 85747 Garching
- Germany
| | - Marina Khaneft
- Jülich Centre for Neutron Science JCNS
- Forschungszentrum Jülich GmbH, Outstation at MLZ
- 85747 Garching
- Germany
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum
- Technische Universität München
- 85747 Garching
- Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS
- Forschungszentrum Jülich GmbH
- 52425 Jülich
- Germany
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18
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc 2016; 138:11714-26. [PMID: 27583570 PMCID: PMC5597961 DOI: 10.1021/jacs.6b05917] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.
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Affiliation(s)
- Alessandro Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madeleine B. Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anja Schüler
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Klaus Gast
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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20
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Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
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Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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21
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Human adenosine A2A receptor binds calmodulin with high affinity in a calcium-dependent manner. Biophys J 2015; 108:903-917. [PMID: 25692595 DOI: 10.1016/j.bpj.2014.12.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/02/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding how ligands bind to G-protein-coupled receptors and how binding changes receptor structure to affect signaling is critical for developing a complete picture of the signal transduction process. The adenosine A2A receptor (A2AR) is a particularly interesting example, as it has an exceptionally long intracellular carboxyl terminus, which is predicted to be mainly disordered. Experimental data on the structure of the A2AR C-terminus is lacking, because published structures of A2AR do not include the C-terminus. Calmodulin has been reported to bind to the A2AR C-terminus, with a possible binding site on helix 8, next to the membrane. The biological meaning of the interaction as well as its calcium dependence, thermodynamic parameters, and organization of the proteins in the complex are unclear. Here, we characterized the structure of the A2AR C-terminus and the A2AR C-terminus-calmodulin complex using different biophysical methods, including native gel and analytical gel filtration, isothermal titration calorimetry, NMR spectroscopy, and small-angle X-ray scattering. We found that the C-terminus is disordered and flexible, and it binds with high affinity (Kd = 98 nM) to calmodulin without major conformational changes in the domain. Calmodulin binds to helix 8 of the A2AR in a calcium-dependent manner that can displace binding of A2AR to lipid vesicles. We also predicted and classified putative calmodulin-binding sites in a larger group of G-protein-coupled receptors.
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22
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Kikhney AG, Svergun DI. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 2015; 589:2570-7. [PMID: 26320411 DOI: 10.1016/j.febslet.2015.08.027] [Citation(s) in RCA: 392] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/17/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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24
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Anunciado D, Rai DK, Qian S, Urban V, O'Neill H. Small-angle neutron scattering reveals the assembly of alpha-synuclein in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1881-1889. [PMID: 26321599 DOI: 10.1016/j.bbapap.2015.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022]
Abstract
The aggregation of α-synuclein (asyn), an intrinsically disordered protein (IDP), is a hallmark in Parkinson's disease (PD). We investigated the conformational changes that asyn undergoes in the presence of membrane and membrane mimetics using small-angle neutron scattering (SANS). In solution, asyn is monomeric and unfolded assuming an ensemble of conformers spanning extended and compact conformations. Using the contrast variation technique and SANS, the protein scattering signal in the membrane-protein complexes is selectively highlighted in order to monitor its conformational changes in this environment. We showed that in the presence of phospholipid membranes asyn transitions from a monodisperse state to aggregated structures with sizes ranging from 200 to 900Å coexisting with the monomeric species. Detailed SANS data analysis revealed that asyn aggregates have a hierarchical organization in which clusters of smaller asyn aggregates assemble to form the larger structures. This study provides new insight into the mechanism of asyn aggregation. We propose an aggregation mechanism in which stable asyn aggregates seed the aggregation process and hence the hierarchical assembly of structures. Our findings demonstrate that membrane-induced conformational changes in asyn lead to its heterogeneous aggregation which could be physiologically relevant in its function or in the diseased state.
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Affiliation(s)
- Divina Anunciado
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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25
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Chukhlieb M, Raasakka A, Ruskamo S, Kursula P. The N-terminal cytoplasmic domain of neuregulin 1 type III is intrinsically disordered. Amino Acids 2015; 47:1567-77. [PMID: 25944317 DOI: 10.1007/s00726-015-1998-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Axonally expressed neuregulin 1 (NRG1) type III is a transmembrane protein involved in various neurodevelopmental processes, including myelination and Schwann cell migration. NRG1 type III has one transmembrane domain and a C-terminal extracellular segment, which contains an epidermal growth factor homology domain. Little is known, however, about the intracellular N terminus of NRG1 type III, and the structure-function relationships of this cytoplasmic domain have remained uncharacterized. In the current study, we carried out the first structural and functional studies on the NRG1 type III cytoplasmic domain. Based on sequence analyses, the domain is predicted to be largely disordered, while a strictly conserved region close to the transmembrane segment may contain helical structure and bind metal ions. As shown by synchrotron radiation circular dichroism spectroscopy, the recombinant NRG1 type III cytoplasmic domain was disordered in solution, but it was able to fold partially into a helical structure, especially when both metals and membrane-mimicking compounds were present. NRG1 cytoplasmic tail binding to metals was further confirmed by calorimetry. These results suggest that the juxtamembrane segment of the NRG1 type III cytoplasmic domain may fold onto the membrane surface upon metal binding. Using synchrotron small-angle X-ray scattering, we further proved that the NRG1 cytoplasmic domain is intrinsically disordered, highly elongated, and behaves like a random polymer. Our work provides the first biochemical and biophysical data on the previously unexplored cytoplasmic domain of NRG1 type III, which will help elucidate the detailed structure-function relationships of this domain.
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Affiliation(s)
- Maryna Chukhlieb
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
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26
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Pilkington GA, Pedersen JS, Briscoe WH. Dendrimer nanofluids in the concentrated regime: from polymer melts to soft spheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3333-3342. [PMID: 25723405 DOI: 10.1021/la504870f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding dendrimer structures and their interactions in concentrated solutions is important to a wide range of applications, such as drug delivery and lubrication. However, controversy has persisted concerning whether, when confined to proximity, dendrimers would entangle as observed for polymer systems, or act as deformable spheres. Furthermore, how such behavior may be related to their size-dependent molecular architecture remains unclear. Using small-angle X-ray scattering (SAXS), the intermolecular interactions and structures in aqueous nanofluids containing three generations of carboxyl-terminated poly(amidoamine) (PAMAM) dendrimers (G0.5, Rg = 9.3 Å; G3.5, Rg = 22.6 Å; G5.5, Rg = 39.9 Å, where Rg is the radius of gyration) over a mass fraction range 0.005 ≤ x ≤ 0.316 have been studied. In the highly concentrated regime (x ≥ 0.157), we observe that the solution properties depend on the dendrimer generation. Our results suggest that the smaller G0.5 dendrimers form a highly entangled polymer melt, while the larger dendrimers, G3.5 and G5.5, form densely packed and ordered structures, in which the individual dendrimers exhibit some degree of mutual overlap or deformation. Our results demonstrate the tunability of interdendrimer interactions via their molecular architecture, which in turn may be harnessed to control and tailor the physical properties of dendrimer nanofluids.
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Affiliation(s)
- Georgia A Pilkington
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Jan S Pedersen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Wuge H Briscoe
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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27
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Hong L, Petridis L, Smith JC. Biomolecular Structure and Dynamics with Neutrons: The View from Simulation. Isr J Chem 2014. [DOI: 10.1002/ijch.201300137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ruskamo S, Chukhlieb M, Vahokoski J, Bhargav SP, Liang F, Kursula I, Kursula P. Juxtanodin is an intrinsically disordered F-actin-binding protein. Sci Rep 2012; 2:899. [PMID: 23198089 PMCID: PMC3509349 DOI: 10.1038/srep00899] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 10/15/2012] [Indexed: 11/13/2022] Open
Abstract
Juxtanodin, also called ermin, is an F-actin-binding protein expressed by oligodendrocytes, the myelin-forming cells of the central nervous system. While juxtanodin carries a short conserved F-actin-binding segment at its C terminus, it otherwise shares no similarity with known protein sequences. We carried out a structural characterization of recombinant juxtanodin in solution. Juxtanodin turned out to be intrinsically disordered, as evidenced by conventional and synchrotron radiation CD spectroscopy. Small-angle X-ray scattering indicated that juxtanodin is a monomeric, highly elongated, unfolded molecule. Ensemble optimization analysis of the data suggested also the presence of more compact forms of juxtanodin. The C terminus was a strict requirement for co-sedimentation of juxtanodin with microfilaments, but juxtanodin had only mild effects on actin polymerization. The disordered nature of juxtanodin may predict functions as a protein interaction hub, although F-actin is its only currently known binding partner.
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Affiliation(s)
- Salla Ruskamo
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Maryna Chukhlieb
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Juha Vahokoski
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | | | - Fengyi Liang
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Inari Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology - Helmholtz Centre for Infection Research (CSSB-HZI); Department of Chemistry, University of Hamburg; and German Electron Synchrotron (DESY), Hamburg, Germany
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology - Helmholtz Centre for Infection Research (CSSB-HZI); Department of Chemistry, University of Hamburg; and German Electron Synchrotron (DESY), Hamburg, Germany
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29
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Sim AYL, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:021901. [PMID: 23005779 DOI: 10.1103/physreve.86.021901] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Indexed: 06/01/2023]
Abstract
Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.
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Affiliation(s)
- Adelene Y L Sim
- Applied Physics Department, Stanford University, Stanford, California 94305, USA
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30
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Leyrat C, Schneider R, Ribeiro EA, Yabukarski F, Yao M, Gérard FCA, Jensen MR, Ruigrok RWH, Blackledge M, Jamin M. Ensemble structure of the modular and flexible full-length vesicular stomatitis virus phosphoprotein. J Mol Biol 2012; 423:182-97. [PMID: 22789567 DOI: 10.1016/j.jmb.2012.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/15/2012] [Accepted: 07/01/2012] [Indexed: 01/10/2023]
Abstract
The phosphoprotein (P) is an essential component of the viral replication machinery of non-segmented negative-strand RNA viruses, connecting the viral polymerase to its nucleoprotein-RNA template and acting as a chaperone of the nucleoprotein by preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of vesicular stomatitis virus (VSV) forms homodimers and possesses a modular organization comprising two stable, well-structured domains concatenated with two intrinsically disordered regions. Here, we used a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering to depict VSV P as an ensemble of continuously exchanging conformers that captures the dynamic character of this protein. We discuss the implications of the dynamics and the large conformational space sampled by VSV P in the assembly and functioning of the viral transcription/replication machinery.
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Affiliation(s)
- Cédric Leyrat
- Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, 38042 Grenoble Cedex 9, France
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31
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Gibrat G, Assairi L, Craescu CT, Hui Bon Hoa G, Loew D, Lombard B, Blouquit L, Bellissent-Funel MC. Use of SANS and biophysical techniques to reveal subtle conformational differences between native apo-calmodulin and its unfolded states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1097-106. [PMID: 22709575 DOI: 10.1016/j.bbapap.2012.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 05/24/2012] [Accepted: 06/01/2012] [Indexed: 11/16/2022]
Abstract
Apo-calmodulin, a small, mainly α, soluble protein is a calcium-dependent protein activator. It is made of two N- and C-terminal domains having a sequence homology of 70%, an identical folding but different stabilities, and is thus an interesting system for unfolding studies. The use of small angle neutron scattering (SANS) and other biophysical techniques has permitted to reveal conformational difference between native and thermal denatured states of apo-calmodulin. The results show that secondary and tertiary structures of apo-calmodulin evolve in a synchronous way, indicating the absence in the unfolding pathway of molten-globule state sufficiently stable to affect transition curves. From SANS experiments, at 85 °C, apo-calmodulin adopts a polymer chain conformation with some residual local structures. After cooling down, apo-calmodulin recovers a compact state, with a secondary structure close to the native one but with a higher radius of gyration and a different tyrosine environment. In fact on a timescale of few minutes, heat denaturation of apo-calmodulin is partially reversible, but on a time scale of hours (for SANS experiments), the long exposure to heat may lead to a non-reversibility due to some chemical perturbation of the protein. In fact, from Mass Spectrometry measurements, we got evidence of dehydration and deamidation of heated apo-calmodulin.
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32
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Wu Y, Pramanik G, Eisele K, Weil T. Convenient Approach to Polypeptide Copolymers Derived from Native Proteins. Biomacromolecules 2012; 13:1890-8. [DOI: 10.1021/bm300418r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yuzhou Wu
- Institute for Organic
Chemistry
III/Macromolecular Chemistry, Ulm University, Albert-Einstein-Allee 11, 89073 Ulm, Germany
| | - Goutam Pramanik
- Institute for Organic
Chemistry
III/Macromolecular Chemistry, Ulm University, Albert-Einstein-Allee 11, 89073 Ulm, Germany
| | - Klaus Eisele
- Institute for Organic
Chemistry
III/Macromolecular Chemistry, Ulm University, Albert-Einstein-Allee 11, 89073 Ulm, Germany
| | - Tanja Weil
- Institute for Organic
Chemistry
III/Macromolecular Chemistry, Ulm University, Albert-Einstein-Allee 11, 89073 Ulm, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
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33
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Gabel F. Small angle neutron scattering for the structural study of intrinsically disordered proteins in solution: a practical guide. Methods Mol Biol 2012; 896:123-135. [PMID: 22821521 DOI: 10.1007/978-1-4614-3704-8_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Small angle neutron scattering (SANS) allows studying bio-macromolecular structures and interactions in solution. It is particularly well-suited to study structural properties of intrinsically disordered proteins (IDPs) over a wide range of length-scales ranging from global aspects (radii of gyration and molecular weight) down to short-distance properties (e.g., cross-sectional analysis). In this book chapter, we provide a practical guide on how to carry out SANS experiments on IDPs and discuss the complementary aspects and strengths of SANS with respect to small angle X-ray scattering (SAXS).
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Affiliation(s)
- Frank Gabel
- Institut de Biologie Structurale Jean-Pierre Ebel. UMR 5075 (CNRS, CEA, UJF), Grenoble, France.
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34
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Silva JC, Borges JC, Cyr DM, Ramos CHI, Torriani IL. Central domain deletions affect the SAXS solution structure and function of yeast Hsp40 proteins Sis1 and Ydj1. BMC STRUCTURAL BIOLOGY 2011; 11:40. [PMID: 22011374 PMCID: PMC3236591 DOI: 10.1186/1472-6807-11-40] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 10/19/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Ydj1 and Sis1 are structurally and functionally distinct Hsp40 proteins of the yeast cytosol. Sis1 is an essential gene whereas the ydj1 gene is essential for growth at elevated temperatures and cannot complement sis1 gene deletion. Truncated polypeptides capable of complementing the sis1 gene deletion comprise the J-domain of either Sis1 or Ydj1 connected to the G/F region of Sis1 (but not Ydj1). Sis1 mutants in which the G/F was deleted but G/M maintained were capable of complementing the sis1 gene deletion. RESULTS To investigate the relevance of central domains on the structure and function of Ydj1 and Sis1 we prepared Sis1 constructs deleting specific domains. The mutants had decreased affinity for heated luciferase but were equally capable of stimulating ATPase activity of Hsp70. Detailed low resolution structures were obtained and the overall flexibility of Hsp40 and its mutants were assessed using SAXS methods. Deletion of either the G/M or the G/M plus CTDI domains had little impact on the quaternary structure of Sis1 analyzed by the SAXS technique. However, deletion of the ZFLR-CTDI changed the relative position of the J-domains in Ydj1 in such a way that they ended up resembling that of Sis1. The results revealed that the G/F and G/M regions are not the only flexible domains. All model structures exhibit a common clamp-like conformation. CONCLUSIONS Our results suggest that the central domains, previously appointed as important features for substrate binding, are also relevant keeping the J-domains in their specific relative positions. The clamp-like architecture observed seems also to be favorable to the interactions of Hsp40 with Hsp70.
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Affiliation(s)
- Julio C Silva
- Department of Condensed Matter Physics, "Gleb Wataghin" Physics Institute, State University of Campinas (UNICAMP), Campinas, SP 13083-859, Brazil
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
- European Synchrotron Radiation Facility, Grenoble, France
| | - Julio C Borges
- Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, SP 13.560-970, Brazil
| | - Douglas M Cyr
- Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Carlos HI Ramos
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas UNICAMP, SP 13083-970, Brazil
| | - Iris L Torriani
- Department of Condensed Matter Physics, "Gleb Wataghin" Physics Institute, State University of Campinas (UNICAMP), Campinas, SP 13083-859, Brazil
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
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35
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Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase. J Mol Biol 2011; 413:639-56. [DOI: 10.1016/j.jmb.2011.08.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 08/20/2011] [Accepted: 08/22/2011] [Indexed: 11/20/2022]
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Bernadó P, Svergun DI. Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. MOLECULAR BIOSYSTEMS 2011; 8:151-67. [PMID: 21947276 DOI: 10.1039/c1mb05275f] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small-angle scattering of X-rays (SAXS) is an established method to study the overall structure and structural transitions of biological macromolecules in solution. For folded proteins, the technique provides three-dimensional low resolution structures ab initio or it can be used to drive rigid-body modeling. SAXS is also a powerful tool for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs), and is highly complementary to the high resolution methods of X-ray crystallography and NMR. Here we present the basic principles of SAXS and review the main approaches to the characterization of IDPs and flexible multidomain proteins using SAXS. Together with the standard approaches based on the analysis of overall parameters, a recently developed Ensemble Optimization Method (EOM) is now available. The latter method allows for the co-existence of multiple protein conformations in solution compatible with the scattering data. Analysis of the selected ensembles provides quantitative information about flexibility and also offers insights into structural features. Examples of the use of SAXS and combined approaches with NMR, X-ray crystallography, and computational methods to characterize completely or partially disordered proteins are presented.
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Affiliation(s)
- Pau Bernadó
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain.
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37
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Pingali SV, O'Neill HM, McGaughey J, Urban VS, Rempe CS, Petridis L, Smith JC, Evans BR, Heller WT. Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity. J Biol Chem 2011; 286:32801-9. [PMID: 21784865 DOI: 10.1074/jbc.m111.263004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolase I (Cel7A) of the fungus Trichoderma reesei (now classified as an anamorph of Hypocrea jecorina) hydrolyzes crystalline cellulose to soluble sugars, making it of key interest for producing fermentable sugars from biomass for biofuel production. The activity of the enzyme is pH-dependent, with its highest activity occurring at pH 4-5. To probe the response of the solution structure of Cel7A to changes in pH, we measured small angle neutron scattering of it in a series of solutions having pH values of 7.0, 6.0, 5.3, and 4.2. As the pH decreases from 7.0 to 5.3, the enzyme structure remains well defined, possessing a spatial differentiation between the cellulose binding domain and the catalytic core that only changes subtly. At pH 4.2, the solution conformation of the enzyme changes to a structure that is intermediate between a properly folded enzyme and a denatured, unfolded state, yet the secondary structure of the enzyme is essentially unaltered. The results indicate that at the pH of optimal activity, the catalytic core of the enzyme adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted and suggest that the increased range of structures afforded by this disordered state plays an important role in the increased activity of Cel7A through conformational selection.
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Affiliation(s)
- Sai Venkatesh Pingali
- Center for Structural Molecular Biology, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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38
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Cousin F, Gummel J, Clemens D, Grillo I, Boué F. Multiple scale reorganization of electrostatic complexes of poly(styrenesulfonate) and lysozyme. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:7078-7085. [PMID: 20073532 DOI: 10.1021/la904398z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on a SANS investigation into the potential for these structural reorganization of complexes composed of lysozyme and small PSS chains of opposite charge if the physicochemical conditions of the solutions are changed after their formation. Mixtures of solutions of lysozyme and PSS with high matter content and with an introduced charge ratio [-]/[+](intro) close to the electrostatic stoichiometry lead to suspensions that are macroscopically stable. They are composed at local scale of dense globular primary complexes of radius approximately 100 A; at a higher scale they are organized fractally with a dimension 2.1. We first show that the dilution of the solution of complexes, all other physicochemical parameters remaining constant, induces a macroscopic destabilization of the solutions but does not modify the structure of the complexes at submicronic scales. This suggests that the colloidal stability of the complexes can be explained by the interlocking of the fractal aggregates in a network at high concentration: dilution does not break the local aggregate structure, but it does destroy the network. We show, second, that the addition of salt does not change the almost frozen inner structure of the cores of the primary complexes, although it does encourage growth of the complexes; these coalesce into larger complexes as salt has partially screened the electrostatic repulsions between two primary complexes. These larger primary complexes remain aggregated with a fractal dimension of 2.1. Third, we show that the addition of PSS chains up to [-]/[+](intro) approximately 20, after the formation of the primary complex with a [-]/[+](intro) close to 1, only slightly changes the inner structure of the primary complexes. Moreover, in contrast to the synthesis achieved in the one-step mixing procedure where the proteins are unfolded for a range of [-]/[+](intro), the native conformation of the proteins is preserved inside the frozen core.
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Affiliation(s)
- Fabrice Cousin
- Laboratoire Léon Brillouin, CEA Saclay 91191 Gif sur Yvette, Cedex, France.
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39
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Makarov DE. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes. J Chem Phys 2010; 132:035104. [DOI: 10.1063/1.3284509] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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41
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Le Coeur C, Demé B, Longeville S. Compression of random coils due to macromolecular crowding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:031910. [PMID: 19391974 DOI: 10.1103/physreve.79.031910] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Indexed: 05/27/2023]
Abstract
The conformation of a linear polymer chain is studied as a function of the concentration of a macromolecular crowding agent by neutron scattering. Excluded volume to random coil due to macromolecular crowding in cells is predicted to exert a compressive force that will tend to reduce its size. It is shown that when reducing free volume due to macromolecular crowding, we observe a compression of the polymer chain with a reduction in its radius of gyration of up to approximately 30% and that the effective chain-chain interactions are strongly modified.
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Affiliation(s)
- C Le Coeur
- Laboratoire Léon Brillouin, CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France
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42
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Lanza DCF, Silva JC, Assmann EM, Quaresma AJC, Bressan GC, Torriani IL, Kobarg J. Human FEZ1 has characteristics of a natively unfolded protein and dimerizes in solution. Proteins 2009; 74:104-21. [PMID: 18615714 DOI: 10.1002/prot.22135] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The fasciculation and elongation protein Zeta 1 (FEZ1) is the mammalian orthologue of the Caenorhabditis elegans protein UNC-76, which is necessary for axon growth. Human FEZ1 interacts with Protein Kinase C (PKC) and several regulatory proteins involved in functions ranging from microtubule associated transport to transcriptional regulation. Theoretical prediction, circular dichroism, fluorescence spectroscopy, and limited proteolysis of recombinant FEZ1 suggest that it contains disordered regions, especially in its N-terminal region, and that it may belong to the group of natively unfolded proteins. Small angle X-ray scattering experiments indicated a mainly disordered conformation, proved that FEZ1 is a dimer of elongated shape and provided overall dimensional parameters for the protein. In vitro pull down experiments confirmed these results and demonstrated that dimerization involves the N-terminus. Ab-initio 3D low resolution models of the full-length conformation of the dimeric constructs 6xHis-FEZ1(1-392) and 6xHis-FEZ1(1-227) were obtained. Furthermore, we performed in vitro phosphorylation assays of FEZ1 with PKC. The phosphorylation occurred mainly in its C-terminal region, and does not cause any significant conformational changes, but nonetheless inhibited its interaction with the FEZ1 interacting domain of the protein CLASP2 in vitro. The C terminus of FEZ1 has been reported to bind to several interacting proteins. This suggests that FEZ1 binding and transport function of interacting proteins may be subject to regulation by phosphorylation.
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McCarney ER, Kohn JE, Plaxco KW. Is There or Isn't There? The Case for (and Against) Residual Structure in Chemically Denatured Proteins. Crit Rev Biochem Mol Biol 2008; 40:181-9. [PMID: 16126485 DOI: 10.1080/10409230591008143] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
First raised some 60 years ago, the question of whether chemically denatured proteins are fully unfolded has, in recent years, seen significantly renewed interest. This increased attention has been spurred, in large part, by new spectroscopic and computational approaches that suggest even the most highly denatured polypeptides contain significant residual structure. In contrast, the most recent scattering results uphold the long-standing view that chemically denatured proteins adopt random coil configurations. Here we review the evidence both for and against residual structure in chemically denatured proteins, and attempt to reconcile these seemingly contradictory observations.
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Affiliation(s)
- Evan R McCarney
- Department of Chemistry and Biochemistry, University of California, Santa Barbara Santa, Barbara, CA 93106, USA
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44
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Bressan GC, Silva JC, Borges JC, Dos Passos DO, Ramos CHI, Torriani IL, Kobarg J. Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein. J Proteome Res 2008; 7:4465-74. [PMID: 18788774 DOI: 10.1021/pr8005342] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human protein Ki-1/57 was first identified through the cross reactivity of the anti-CD30 monoclonal antibody Ki-1, in Hodgkin lymphoma cells. The expression of Ki-1/57 in diverse cancer cells and its phosphorylation in peripheral blood leukocytes after mitogenic activation suggested its possible role in cell signaling. Ki-1/57 interacts with several other regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism, suggesting it may have pleiotropic functions. In a previous spectroscopic analysis, we observed a low content of secondary structure for Ki-1/57 constructs. Here, Circular dichroism experiments, in vitro RNA binding analysis, and limited proteolysis assays of recombinant Ki-1/57(122-413) and proteolysis assays of endogenous full length protein from human HEK293 cells suggested that Ki-1/57 has characteristics of an intrinsically unstructured protein. Small-angle X-ray scattering (SAXS) experiments were performed with the C-terminal fragment Ki-1/57(122-413). These results indicated an elongated shape and a partially unstructured conformation of the molecule in solution, confirming the characteristics of an intrinsically unstructured protein. Experimental curves together with ab initio modeling approaches revealed an extended and flexible molecule in solution. An elongated shape was also observed by analytical gel filtration. Furthermore, sedimentation velocity analysis suggested that Ki-1/57 is a highly asymmetric protein. These findings may explain the functional plasticity of Ki-1/57, as suggested by the wide array of proteins with which it is capable of interacting in yeast two-hybrid interaction assays.
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Affiliation(s)
- Gustavo C Bressan
- National Synchrotron Light Laboratory - LNLS, 13083-970, Campinas, SP, Brazil
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45
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Abstract
The clathrin triskelion, which is a three-legged pinwheel-shaped heteropolymer, is a major component in the protein coats of certain post-Golgi and endocytic vesicles. At low pH, or at physiological pH in the presence of assembly proteins, triskelia will self-assemble to form a closed clathrin cage, or "basket". Recent static light scattering and dynamic light scattering studies of triskelia in solution showed that an individual triskelion has an intrinsic pucker similar to, but differing from, that inferred from a high resolution cryoEM structure of a triskelion in a clathrin basket. We extend the earlier solution studies by performing small-angle neutron scattering (SANS) experiments on isolated triskelia, allowing us to examine a higher q range than that probed by static light scattering. Results of the SANS measurements are consistent with the light scattering measurements, but show a shoulder in the scattering function at intermediate q values (0.016 A(-1)), just beyond the Guinier regime. This feature can be accounted for by Brownian dynamics simulations based on flexible bead-spring models of a triskelion, which generate time-averaged scattering functions. Calculated scattering profiles are in good agreement with the experimental SANS profiles when the persistence length of the assumed semiflexible triskelion is close to that previously estimated from the analysis of electron micrographs.
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46
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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 2008; 40:191-285. [PMID: 18078545 DOI: 10.1017/s0033583507004635] [Citation(s) in RCA: 845] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein-nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.
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47
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Leggio C, Galantini L, Pavel NV. About the albumin structure in solution: cigar Expanded form versus heart Normal shape. Phys Chem Chem Phys 2008; 10:6741-50. [DOI: 10.1039/b808938h] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Beaufils S, Hadaoui-Hammoutène R, Vié V, Miranda G, Perez J, Terriac E, Henry G, Delage MM, Léonil J, Martin P, Renault A. Comparative behaviour of goat β and αs1-caseins at the air–water interface and in solution. Food Hydrocoll 2007. [DOI: 10.1016/j.foodhyd.2006.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Roque A, Ponte I, Suau P. Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1. Biophys J 2007; 93:2170-7. [PMID: 17513371 PMCID: PMC1959549 DOI: 10.1529/biophysj.107.104513] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We studied the secondary structure of the C-terminal domains of the histone H1 subtypes H1 degrees (C-H1 degrees ) and H1t (C-H1t) in the presence of macromolecular crowding agents (Ficoll 70 and PEG 6000) by IR spectroscopy. The carboxyl-terminal domain has little structure in aqueous solution but became extensively folded in the presence of crowding agents. In 30% PEG, C-H1 degrees contained 19% alpha-helix, 28% beta-sheet, 16% turns, and 31% open loops. Similar proportions were observed in 30% Ficoll 70 and for C-H1t in both crowding agents. The proportions of secondary structure motifs were comparable to those of the DNA-bound domain. Kratky plots of the small-angle x-ray scattering showed that in crowding agents the C-terminus had the compaction of a globular state. Progressive dissipation of the secondary structure and a linear increase in partial heat capacity with temperature together with increased binding of ANS indicated that the C-terminus is not cooperatively folded in crowded conditions. Native-like secondary structure and compactness in absence of folding cooperativity indicate that the C-terminus in crowding agents is in a molten globule state. Folding of the C-terminus in crowded conditions may increase the rate of the transition toward the DNA-bound state and facilitate H1 diffusion inside cell nuclei.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Aschi A, Gharbi A, Daoud M, Douillard R, Calmettes P. Study of structure and scaling behavior of chemically unfolded β-casein by means of small-angle neutron scattering. POLYM INT 2007. [DOI: 10.1002/pi.2176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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