151
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Glover K, Li Y, Mukhopadhyay S, Leuthner Z, Chakravarthy S, Colbert CL, Sinha SC. Structural transitions in conserved, ordered Beclin 1 domains essential to regulating autophagy. J Biol Chem 2017; 292:16235-16248. [PMID: 28798234 DOI: 10.1074/jbc.m117.804195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/20/2017] [Indexed: 01/10/2023] Open
Abstract
Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves sequestration of selected cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an "overlap helix" (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal β-α repeated, autophagy-specific domain (BARAD). Here, using CD spectroscopy, isothermal titration calorimetry, and small-angle X-ray scattering, we show that in the homodimeric state, the OH transitions between these two different packing states, with the predominant state comprising the OH packed against the BARAD, contrary to expectations based on known BECN1 interactions with heterologous partners. We confirmed this observation by comparing the impact of mutating four residues that mediate packing of the OH against both the CCD and BARAD on structure and stability of the CCD, the OH+BARAD, and the two-domain CCD-BARAD. Last, we used cellular assays to demonstrate that mutation of these OH-interface residues abrogates starvation-induced up-regulation of autophagy but does not affect basal autophagy. In summary, we have identified a BECN1 helical region that transitions between packing as part of either one of two conserved domains (i.e. the CCD or the BARAD). Our findings have important implications for the relative stability of autophagy-inactive and autophagy-active BECN1 complexes.
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Affiliation(s)
- Karen Glover
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Yue Li
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Shreya Mukhopadhyay
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Zoe Leuthner
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | | | - Christopher L Colbert
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Sangita C Sinha
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
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152
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Vazquez L, e Lima LMTDR, Almeida MDS. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. PLoS One 2017; 12:e0182132. [PMID: 28750053 PMCID: PMC5531528 DOI: 10.1371/journal.pone.0182132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
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Affiliation(s)
- Leonardo Vazquez
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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153
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Singal B, Balakrishna AM, Nartey W, Manimekalai MSS, Jeyakanthan J, Grüber G. Crystallographic and solution structure of the N-terminal domain of the Rel protein fromMycobacterium tuberculosis. FEBS Lett 2017; 591:2323-2337. [DOI: 10.1002/1873-3468.12739] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Bharti Singal
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
| | | | - Wilson Nartey
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
| | | | | | - Gerhard Grüber
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
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154
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Dahal E, Choi M, Alam N, Bhirde AA, Beaucage SL, Badano A. Structural evaluation of an amyloid fibril model using small-angle x-ray scattering. Phys Biol 2017; 14:046001. [DOI: 10.1088/1478-3975/aa776a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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155
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Huang Z, Kangovi GN, Wen W, Lee S, Niu L. An RNA Aptamer Capable of Forming a Hydrogel by Self-Assembly. Biomacromolecules 2017; 18:2056-2063. [PMID: 28609610 DOI: 10.1021/acs.biomac.7b00314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogels are supramolecular assemblies with both solute transport properties like liquids and mechanical properties like elastomers. To date, every type of biomolecules except ribonucleic acid (RNA), is capable of forming a hydrogel. Here, we report an RNA that forms a hydrogel by self-assembly. This RNA is originally identified by systematic evolution of ligands by exponential enrichment (SELEX) to enhance the activity of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors as a potential RNA drug for the treatment of cognitive disorders. The RNA hydrogel exhibits an elastic modulus plateau on the order of 102 Pa and shows dynamic RNA chain interactions with relaxation behaviors similar to living wormlike micellar solutions. Small-angle X-ray scattering and cryogenic electron microscopy characterization support the RNA network structures. By sequence mutation and rheological measurements, we reveal two key sequence motifs in the RNA responsible for intermolecular recognition and the formation of a polymer network by self-assembly.
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Affiliation(s)
- Zhen Huang
- Chemistry Department, University at Albany, State University of New York , Albany, New York 12222, United States
| | - Gagan N Kangovi
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Wei Wen
- Chemistry Department, University at Albany, State University of New York , Albany, New York 12222, United States
| | - Sangwoo Lee
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Li Niu
- Chemistry Department, University at Albany, State University of New York , Albany, New York 12222, United States
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156
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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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157
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Galeano BK, Ranatunga W, Gakh O, Smith DY, Thompson JR, Isaya G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers. Metallomics 2017; 9:773-801. [PMID: 28548666 PMCID: PMC5552075 DOI: 10.1039/c7mt00089h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/02/2017] [Indexed: 02/06/2023]
Abstract
Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.
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Affiliation(s)
- B. K. Galeano
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Graduate School of Biomedical Sciences , Rochester , Minnesota , USA
| | - W. Ranatunga
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - O. Gakh
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - D. Y. Smith
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - J. R. Thompson
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
| | - G. Isaya
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
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158
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Müller JP, Löf A, Mielke S, Obser T, Bruetzel LK, Vanderlinden W, Lipfert J, Schneppenheim R, Benoit M. pH-Dependent Interactions in Dimers Govern the Mechanics and Structure of von Willebrand Factor. Biophys J 2017; 111:312-322. [PMID: 27463134 DOI: 10.1016/j.bpj.2016.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/02/2016] [Accepted: 06/21/2016] [Indexed: 01/12/2023] Open
Abstract
Von Willebrand factor (VWF) is a multimeric plasma glycoprotein that is activated for hemostasis by increased hydrodynamic forces at sites of vascular injury. Here, we present data from atomic force microscopy-based single-molecule force measurements, atomic force microscopy imaging, and small-angle x-ray scattering to show that the structure and mechanics of VWF are governed by multiple pH-dependent interactions with opposite trends within dimeric subunits. In particular, the recently discovered strong intermonomer interaction, which induces a firmly closed conformation of dimers and crucially involves the D4 domain, was observed with highest frequency at pH 7.4, but was essentially absent at pH values below 6.8. However, below pH 6.8, the ratio of compact dimers increased with decreasing pH, in line with a previous transmission electron microscopy study. These findings indicated that the compactness of dimers at pH values below 6.8 is promoted by other interactions that possess low mechanical resistance compared with the strong intermonomer interaction. By investigating deletion constructs, we found that compactness under acidic conditions is primarily mediated by the D4 domain, i.e., remarkably by the same domain that also mediates the strong intermonomer interaction. As our data suggest that VWF has the highest mechanical resistance at physiological pH, local deviations from physiological pH (e.g., at sites of vascular injury) may represent a means to enhance VWF's hemostatic activity where needed.
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Affiliation(s)
- Jochen P Müller
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.
| | - Achim Löf
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Salomé Mielke
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Tobias Obser
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linda K Bruetzel
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany; Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Reinhard Schneppenheim
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Benoit
- Department of Physics and Center for Nanoscience, LMU Munich, Munich, Germany
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159
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Tsirkone VG, Blokken J, De Wit F, Breemans J, De Houwer S, Debyser Z, Christ F, Strelkov SV. N-terminal half of transportin SR2 interacts with HIV integrase. J Biol Chem 2017; 292:9699-9710. [PMID: 28356354 PMCID: PMC5465493 DOI: 10.1074/jbc.m117.777029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/14/2017] [Indexed: 11/06/2022] Open
Abstract
The karyopherin transportin SR2 (TRN-SR2, TNPO3) is responsible for shuttling specific cargoes such as serine/arginine-rich splicing factors from the cytoplasm to the nucleus. This protein plays a key role in HIV infection by facilitating the nuclear import of the pre-integration complex (PIC) that contains the viral DNA as well as several cellular and HIV proteins, including the integrase. The process of nuclear import is considered to be the bottleneck of the viral replication cycle and therefore represents a promising target for anti-HIV drug design. Previous studies have demonstrated that the direct interaction between TRN-SR2 and HIV integrase predominantly involves the catalytic core domain (CCD) and the C-terminal domain (CTD) of the integrase. We aimed at providing a detailed molecular view of this interaction through a biochemical characterization of the respective protein complex. Size-exclusion chromatography was used to characterize the interaction of TRN-SR2 with a truncated variant of the HIV-1 integrase, including both the CCD and CTD. These experiments indicate that one TRN-SR2 molecule can specifically bind one CCD-CTD dimer. Next, the regions of the solenoid-like TRN-SR2 molecule that are involved in the interaction with integrase were identified using AlphaScreen binding assays, revealing that the integrase interacts with the N-terminal half of TRN-SR2 principally through the HEAT repeats 4, 10, and 11. Combining these results with small-angle X-ray scattering data for the complex of TRN-SR2 with truncated integrase, we propose a molecular model of the complex. We speculate that nuclear import of the PIC may proceed concurrently with the normal nuclear transport.
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Affiliation(s)
| | - Jolien Blokken
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Flore De Wit
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | | | - Stéphanie De Houwer
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Zeger Debyser
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Frauke Christ
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
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160
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Rodríguez-Ruiz I, Radajewski D, Charton S, Phamvan N, Brennich M, Pernot P, Bonneté F, Teychené S. Innovative High-Throughput SAXS Methodologies Based on Photonic Lab-on-a-Chip Sensors: Application to Macromolecular Studies. SENSORS (BASEL, SWITZERLAND) 2017; 17:E1266. [PMID: 28574461 PMCID: PMC5492703 DOI: 10.3390/s17061266] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/17/2017] [Accepted: 05/31/2017] [Indexed: 02/04/2023]
Abstract
The relevance of coupling droplet-based Photonic Lab-on-a-Chip (PhLoC) platforms and Small-Angle X-Ray Scattering (SAXS) technique is here highlighted for the performance of high throughput investigations, related to the study of protein macromolecular interactions. With this configuration, minute amounts of sample are required to obtain reliable statistical data. The PhLoC platforms presented in this work are designed to allow and control an effective mixing of precise amounts of proteins, crystallization reagents and buffer in nanoliter volumes, and the subsequent generation of nanodroplets by means of a two-phase flow. Spectrophotometric sensing permits a fine control on droplet generation frequency and stability as well as on concentration conditions, and finally the droplet flow is synchronized to perform synchrotron radiation SAXS measurements in individual droplets (each one acting as an isolated microreactor) to probe protein interactions. With this configuration, droplet physic-chemical conditions can be reproducibly and finely tuned, and monitored without cross-contamination, allowing for the screening of a substantial number of saturation conditions with a small amount of biological material. The setup was tested and validated using lysozyme as a model of study. By means of SAXS experiments, the proteins gyration radius and structure envelope were calculated as a function of protein concentration. The obtained values were found to be in good agreement with previously reported data, but with a dramatic reduction of sample volume requirements compared to studies reported in the literature.
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Affiliation(s)
| | - Dimitri Radajewski
- Laboratoire de Génie Chimique, UMR 5503, 4 allée Emile Monso, 31432 Toulouse, France.
| | | | - Nhat Phamvan
- Laboratoire de Génie Chimique, UMR 5503, 4 allée Emile Monso, 31432 Toulouse, France.
| | - Martha Brennich
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Petra Pernot
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Françoise Bonneté
- Institut des Biomolécules Max-Mousseron, UMR 5247, Université d'Avignon, 33 rue Louis Pasteur, 84000 Avignon, France.
| | - Sébastien Teychené
- Laboratoire de Génie Chimique, UMR 5503, 4 allée Emile Monso, 31432 Toulouse, France.
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161
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Alsarraf H, Dedic E, Bjerrum MJ, Østergaard O, Kristensen MP, Petersen JW, Jørgensen R. Biophysical comparison of diphtheria and tetanus toxins with the formaldehyde-detoxified toxoids, the main components of diphtheria and tetanus vaccines. Virulence 2017; 8:1880-1889. [PMID: 28430538 DOI: 10.1080/21505594.2017.1321726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Husam Alsarraf
- a Department of Microbiology and Infection Control , Statens Serum Institut , Copenhagen S. , Denmark
| | - Emil Dedic
- a Department of Microbiology and Infection Control , Statens Serum Institut , Copenhagen S. , Denmark
| | - Morten J Bjerrum
- b Department of Chemistry , University of Copenhagen , Copenhagen Ø. , Denmark
| | - Ole Østergaard
- c Department of Autoimmunology , Statens Serum Institut , Copenhagen S. , Denmark
| | - Max Per Kristensen
- d Vaccine Development Department , Statens Serum Institut , Copenhagen S. , Denmark
| | - Jesper W Petersen
- e Bacterial Vaccine Department , Statens Serum Institut , Copenhagen S. , Denmark
| | - René Jørgensen
- a Department of Microbiology and Infection Control , Statens Serum Institut , Copenhagen S. , Denmark
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162
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Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics. Arch Biochem Biophys 2017; 628:33-41. [PMID: 28501583 PMCID: PMC5553349 DOI: 10.1016/j.abb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/25/2023]
Abstract
Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions. SAXS and NMR are effective and highly complementary techniques in structural biology. Constraints from SAXS can be readily incorporated in NMR structure calculations. High resolution NMR models of domains can serve as building blocks for SAXS-based rigid body modeling. Flexible systems can be well described using ensemble approaches combining SAXS and NMR. Dynamics studies can be enhanced by combining SAXS and NMR.
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163
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Pan A, Saw WG, Subramanian Manimekalai MS, Grüber A, Joon S, Matsui T, Weiss TM, Grüber G. Structural features of NS3 of Dengue virus serotypes 2 and 4 in solution and insight into RNA binding and the inhibitory role of quercetin. Acta Crystallogr D Struct Biol 2017; 73:402-419. [PMID: 28471365 PMCID: PMC5417341 DOI: 10.1107/s2059798317003849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
Dengue virus (DENV), which has four serotypes (DENV-1 to DENV-4), is the causative agent of the viral infection dengue. DENV nonstructural protein 3 (NS3) comprises a serine protease domain and an RNA helicase domain which has nucleotide triphosphatase activities that are essential for RNA replication and viral assembly. Here, solution X-ray scattering was used to provide insight into the overall structure and flexibility of the entire NS3 and its recombinant helicase and protease domains for Dengue virus serotypes 2 and 4 in solution. The DENV-2 and DENV-4 NS3 forms are elongated and flexible in solution. The importance of the linker residues in flexibility and domain-domain arrangement was shown by the compactness of the individual protease and helicase domains. Swapping of the 174PPAVP179 linker stretch of the related Hepatitis C virus (HCV) NS3 into DENV-2 NS3 did not alter the elongated shape of the engineered mutant. Conformational alterations owing to RNA binding are described in the protease domain, which undergoes substantial conformational alterations that are required for the optimal catalysis of bound RNA. Finally, the effects of ATPase inhibitors on the enzymatically active DENV-2 and DENV-4 NS3 and the individual helicases are presented, and insight into the allosteric effect of the inhibitor quercetin is provided.
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Affiliation(s)
- Ankita Pan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Ardina Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shin Joon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laboratory, Menlo Park, California, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laboratory, Menlo Park, California, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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164
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Pedrini B, Menzel A, Guzenko VA, David C, Abela R, Gutt C. Model-independent particle species disentanglement by X-ray cross-correlation scattering. Sci Rep 2017; 7:45618. [PMID: 28374754 PMCID: PMC5379484 DOI: 10.1038/srep45618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 03/01/2017] [Indexed: 11/09/2022] Open
Abstract
Mixtures of different particle species are often investigated using the angular averages of the scattered X-ray intensity. The number of species is deduced by singular value decomposition methods. The full disentanglement of the data into per-species contributions requires additional knowledge about the system under investigation. We propose to exploit higher-order angular X-ray intensity correlations with a new computational protocol, which we apply to synchrotron data from two-species mixtures of two-dimensional static test nanoparticles. Without any other information besides the correlations, we demonstrate the assessment of particle species concentrations in the measured data sets, as well as the full ab initio reconstruction of both particle structures. The concept extends straightforwardly to more species and to the three-dimensional case, whereby the practical application will require the measurements to be performed at an X-ray free electron laser.
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Affiliation(s)
- B Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - A Menzel
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - V A Guzenko
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - C David
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - R Abela
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - C Gutt
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068, Siegen, Germany
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165
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Guan H, Tian J, Qin B, Wojdyla JA, Wang B, Zhao Z, Wang M, Cui S. Crystal structure of 2C helicase from enterovirus 71. SCIENCE ADVANCES 2017; 3:e1602573. [PMID: 28508043 PMCID: PMC5409451 DOI: 10.1126/sciadv.1602573] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Enterovirus 71 (EV71) is the major pathogen responsible for outbreaks of hand, foot, and mouth disease. EV71 nonstructural protein 2C participates in many critical events throughout the virus life cycle; however, its precise role is not fully understood. Lack of a high-resolution structure made it difficult to elucidate 2C activity and prevented inhibitor development. We report the 2.5 Å-resolution crystal structure of the soluble part of EV71 2C, containing an adenosine triphosphatase (ATPase) domain, a cysteine-rich zinc finger with an unusual fold, and a carboxyl-terminal helical domain. Unlike other AAA+ ATPases, EV71 2C undergoes a carboxyl terminus-mediated self-oligomerization, which is dependent on a specific interaction between the carboxyl-terminal helix of one monomer and a deep pocket formed between the ATPase and the zinc finger domains of the neighboring monomer. The carboxyl terminus-mediated self-oligomerization is fundamental to 2C ATPase activity and EV71 replication. Our findings suggest a strategy for inhibition of enterovirus replication by disruption of the self-oligomerization interface of 2C.
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Affiliation(s)
- Hongxin Guan
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Juan Tian
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Bo Qin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | | | - Bei Wang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Zhendong Zhao
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Meitian Wang
- Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Sheng Cui
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
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166
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Using Small Angle X-Ray Scattering (SAXS) to Characterize the Solution Conformation and Flexibility of Matrix Metalloproteinases (MMPs). Methods Mol Biol 2017. [PMID: 28299734 DOI: 10.1007/978-1-4939-6863-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Small angle X-ray scattering (SAXS) provides information about the conformation and flexibility of proteins in solution, and hence provides complementary structural information to that obtained from X-ray crystallography and nuclear magnetic resonance spectroscopy. In this chapter, we describe the methods for the preparation of matrix metalloproteinase (MMP) samples for SAXS analyses, and for the acquisition, processing and interpretation of the SAXS data.
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167
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Prischi F, Pastore A. Hybrid Methods in Iron-Sulfur Cluster Biogenesis. Front Mol Biosci 2017; 4:12. [PMID: 28349052 PMCID: PMC5346568 DOI: 10.3389/fmolb.2017.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes. We applied this technique to gain insights into the structure of complexes formed amongst proteins involved in the molecular machine, which produces the essential iron-sulfur cluster prosthetic groups. Our results were validated both by X-ray structures and by other groups who adopted the same approach. We discuss the advantages and the limitations of our methodology and propose new avenues, which could improve it.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex Colchester, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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168
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Soper AK, Edler KJ. Coarse-grained empirical potential structure refinement: Application to a reverse aqueous micelle. Biochim Biophys Acta Gen Subj 2017; 1861:1652-1660. [PMID: 28259740 DOI: 10.1016/j.bbagen.2017.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 10/20/2022]
Abstract
Conventional atomistic computer simulations, involving perhaps up to 106atoms, can achieve length-scales on the order of a few 10s of nm. Yet many heterogeneous systems, such as colloids, nano-structured materials, or biological systems, can involve correlations over distances up 100s of nm, perhaps even 1μm in some instances. For such systems it is necessary to invoke coarse-graining, where single atoms are replaced by agglomerations of atoms, usually represented as spheres, in order for the simulation to be performed within a practical computer memory and time scale. Small angle scattering and reflectivity measurements, both X-ray and neutron, are routinely used to investigate structure in these systems, and traditionally the data have been interpreted in terms of discrete objects, such as spheres, sheets, and cylinders, and combinations thereof. Here we combine the coarse-grained computer simulation approach with neutron small angle scattering to refine the structure of a heterogeneous system, in the present case a reverse aqueous micelle of sodium-dioctyl sulfosuccinate (AOT) and iso-octane. The method closely follows empirical potential structure refinement and involves deriving an empirical interaction potential from the scattering data. As in traditional coarse-grained methods, individual atoms are replaced by spherical density profiles, which, unlike real atoms, can inter-penetrate to a significant extent. The method works over an arbitrary range of length-scales, but is limited to around 2 orders of magnitude in distance above a specified dimension. The smallest value for this dimension is of order 1nm, but the largest dimension is arbitrary. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.
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Affiliation(s)
- A K Soper
- STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK.
| | - K J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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169
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Zeng J, Bian F, Wang J, Li X, Wang Y, Tian F, Zhou P. Performance on absolute scattering intensity calibration and protein molecular weight determination at BL16B1, a dedicated SAXS beamline at SSRF. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:509-520. [PMID: 28244448 DOI: 10.1107/s1600577516019135] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
The optical system and end-station of bending-magnet beamline BL16B1, dedicated to small-angle X-ray scattering (SAXS) at the Shanghai Synchrotron Radiation Facility, is described. Constructed in 2009 and upgraded in 2013, this beamline has been open to users since May 2009 and supports methodologies including SAXS, wide-angle X-ray scattering (WAXS), simultaneous SAXS/WAXS, grazing-incidence small-angle X-ray scattering (GISAXS) and anomalous small-angle X-ray scattering (ASAXS). Considering that an increasing necessity for absolute calibration of SAXS intensity has been recognized in in-depth investigations, SAXS intensity is re-stated according to the extent of data processing, and the absolute intensity is suggested to be a unified presentation of SAXS data in this article. Theory with a practical procedure for absolute intensity calibration is established based on BL16B1, using glass carbon and water as primary and secondary standards, respectively. The calibration procedure can be completed in minutes and shows good reliability under different conditions. An empirical line of scale factor estimation is also established for any specific SAXS setup at the beamline. Beamline performance on molecular weight (MW) determination is provided as a straightforward application and verification of the absolute intensity calibration. Results show good accuracy with a deviation of less than 10% compared with the known value, which is also the best attainable accuracy in recent studies using SAXS to measure protein MW. Fast MW measurement following the demonstrated method also enables an instant check or pre-diagnosis of the SAXS performance to improve the data acquisition.
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Affiliation(s)
- Jianrong Zeng
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Fenggang Bian
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Jie Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Xiuhong Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Yuzhu Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Feng Tian
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
| | - Ping Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Zhangheng Road 239, Pudong District, Shanghai 201204, People's Republic of China
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170
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Pham N, Radajewski D, Round A, Brennich M, Pernot P, Biscans B, Bonneté F, Teychené S. Coupling High Throughput Microfluidics and Small-Angle X-ray Scattering to Study Protein Crystallization from Solution. Anal Chem 2017; 89:2282-2287. [DOI: 10.1021/acs.analchem.6b03492] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Nhat Pham
- Laboratoire
de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 allée Emile Monso, 31432 Toulouse, France
| | - Dimitri Radajewski
- Laboratoire
de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 allée Emile Monso, 31432 Toulouse, France
| | - Adam Round
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
- Unit
for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Martha Brennich
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Petra Pernot
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Béatrice Biscans
- Laboratoire
de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 allée Emile Monso, 31432 Toulouse, France
| | - Françoise Bonneté
- Institut
des Biomolécules Max-Mousseron, UMR 5247, Université d’Avignon, 301
rue Baruch de Spinoza, 84000 Avignon, France
| | - Sébastien Teychené
- Laboratoire
de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 4 allée Emile Monso, 31432 Toulouse, France
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171
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Zhang Y, Deng Y, Zhao Y. Structure-based modelling of hemocyanin allergenicity in squid and its response to high hydrostatic pressure. Sci Rep 2017; 7:40021. [PMID: 28112159 PMCID: PMC5256278 DOI: 10.1038/srep40021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 12/01/2016] [Indexed: 11/09/2022] Open
Abstract
The secondary, tertiary, and quaternary structures of squid hemocyanin (Hc) were characterised, and the relationship between Hc structure and allergenicity responses to high hydrostatic pressure (HHP) was modelled. The Hc allergenicity varied with its protein structure. Electrophoresis analysis revealed that HHP treatment significantly decreased the band intensity of Hc when increasing pressure from 200 and 400 MPa to 600 MPa. The protein structure analysis of squid Hc showed that while HHP treatment decreased the α-helix content, free sulfhydryl content, and Rg, it increased the random coil content, surface hydrophobicity index (Ho), Guinier aggregation number (〈Nagg〉G) and average aggregation number (〈Nagg〉Q). The α-helix and random coil contents of the 600 MPa treated samples were 23.67% and 37.54%, respectively, compared to 32.37% and 32.02% in the control, respectively. HHP treatment decreased the IgE and IgG-binding capacities, indicating a significant decrease in the allergenicity (P< 0.05) of squid Hc. This study provided meaningful information of applying HHP to reduce allergenicity, and explained the responses of Hc protein structure to HHP for lowering the allergenicity of squid.
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Affiliation(s)
- Yifeng Zhang
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, SJTU-Bor S. Luh Food Safety Center, Department of Food Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yun Deng
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, SJTU-Bor S. Luh Food Safety Center, Department of Food Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yanyun Zhao
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, SJTU-Bor S. Luh Food Safety Center, Department of Food Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Department of Food Science &Technology, Oregon State University, 100 Wiegand Hall, Corvallis, OR 97331, USA
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172
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Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thor JJ, Ihee H. Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein. Phys Chem Chem Phys 2017; 18:8911-8919. [PMID: 26960811 DOI: 10.1039/c6cp00476h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.
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Affiliation(s)
- Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Cheolhee Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Youngmin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Yang Ouk Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sunhong Jun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Sungjun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago IL 60637, USA
| | - Jasper J van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Korea
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173
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Brown JS, Acevedo YM, He GD, Freed JH, Clancy P, Alabi CA. Synthesis and Solution-Phase Characterization of Sulfonated Oligothioetheramides. Macromolecules 2017; 50:8731-8738. [PMID: 29386690 PMCID: PMC5788177 DOI: 10.1021/acs.macromol.7b01915] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nature has long demonstrated the importance of chemical sequence to induce structure and tune physical interactions. Investigating macromolecular structure and dynamics is paramount to understand macromolecular binding and target recognition. To that end, we have synthesized and characterized flexible sulfonated oligothioetheramides (oligo-TEAs) by variable temperature pulse field gradient (PFG) NMR, double electron-electron resonance (DEER), and molecular dynamics (MD) simulations to capture their room temperature structure and dynamics in water. We have examined the contributions of synthetic length (2-12mer), pendant group charge, and backbone hydrophobicity. We observe significant entropic collapse, driven in part by backbone hydrophobicity. Analysis of individual monomer contributions revealed larger changes due to the backbone compared to pendant groups. We also observe screening of intramolecular electrostatic repulsions. Finally, we comment on the combination of DEER and PFG NMR measurements via Stokes-Einstein-Sutherland diffusion theory. Overall, this sensitive characterization holds promise to enable de novo development of macromolecular structure and sequence-structure-function relationships with flexible, but biologically functional macromolecules.
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Affiliation(s)
- Joseph S. Brown
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Yaset M. Acevedo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Grace D. He
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
| | - Paulette Clancy
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Christopher A. Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
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174
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Shih O, Yeh YQ, Liao KF, Sung TC, Chiang YW, Jeng US. Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution. Phys Chem Chem Phys 2017; 19:7947-7954. [DOI: 10.1039/c6cp08820a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear oligomerization of ditopic BAX-dimers into tri-dimer helical units then into a rod-like structure, as revealed using integrated ESR/SAXS/MD analyses.
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Affiliation(s)
- Orion Shih
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Tai-Ching Sung
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
- Department of Chemical Engineering
- National Tsing Hua University
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175
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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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176
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Leney AC, Heck AJR. Native Mass Spectrometry: What is in the Name? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:5-13. [PMID: 27909974 PMCID: PMC5174146 DOI: 10.1007/s13361-016-1545-3] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 05/11/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein-protein and protein-ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as "native MS," has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure-function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by "native MS," when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions. Graphical Abstract ᅟ.
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Affiliation(s)
- Aneika C Leney
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584CH, Utrecht, The Netherlands.
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177
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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178
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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179
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Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI. Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 2016; 11:2122-2153. [PMID: 27711050 PMCID: PMC5402874 DOI: 10.1038/nprot.2016.113] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume, including the solvent and buffer components, as well as the macromolecules of interest. To obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis, so it is essential that the samples be pure and monodisperse for the duration of the experiment. This protocol outlines the basic physics of SAXS and SANS, and it reveals how the underlying conceptual principles of the techniques ultimately 'translate' into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size-exclusion chromatography (SEC) and light scattering. Also included are procedures that are specific to X-rays (in-line SEC-SAXS) and neutrons, specifically preparing samples for contrast matching or variation experiments and deuterium labeling of proteins.
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Affiliation(s)
- Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - Clément E. Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
| | - David B. Langley
- Victor Chang Cardiac Research and Garvan Institutes, Darlinghurst,
NSW, Australia
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, Lucas
Heights, NSW, Australia
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o
DESY. Hamburg, 22603, Germany
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180
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Potent and selective bivalent inhibitors of BET bromodomains. Nat Chem Biol 2016; 12:1097-1104. [PMID: 27775716 DOI: 10.1038/nchembio.2210] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 09/02/2016] [Indexed: 01/02/2023]
Abstract
Proteins of the bromodomain and extraterminal (BET) family, in particular bromodomain-containing protein 4 (BRD4), are of great interest as biological targets. BET proteins contain two separate bromodomains, and existing inhibitors bind to them monovalently. Here we describe the discovery and characterization of probe compound biBET, capable of engaging both bromodomains simultaneously in a bivalent, in cis binding mode. The evidence provided here was obtained in a variety of biophysical and cellular experiments. The bivalent binding results in very high cellular potency for BRD4 binding and pharmacological responses such as disruption of BRD4-mediator complex subunit 1 foci with an EC50 of 100 pM. These compounds will be of considerable utility as BET/BRD4 chemical probes. This work illustrates a novel concept in ligand design-simultaneous targeting of two separate domains with a drug-like small molecule-providing precedent for a potentially more effective paradigm for developing ligands for other multi-domain proteins.
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181
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Amdursky N. Photoacids as a new fluorescence tool for tracking structural transitions of proteins: following the concentration-induced transition of bovine serum albumin. Phys Chem Chem Phys 2016; 17:32023-32. [PMID: 26573990 DOI: 10.1039/c5cp05548b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Spectroscopy-based techniques for assessing structural transitions of proteins follow either an intramolecular chromophore, as in absorption-based circular dichroism (CD) or fluorescence-based tryptophan emission, or an intermolecular chromophore such as fluorescent probes. Here a new fluorescent probe method to probe the structural transition of proteins by photoacids is presented, which has a fundamentally different photo-physical origin to that of common fluorescent probes. Photoacids are molecules that release a proton upon photo-excitation. By following the steady-state and time-resolved emission of the protonated and de-protonated species of the photoacid we probe the environment of its binding site in bovine serum albumin (BSA) in a wide range of weight concentrations (0.001-8%). We found a unique concentration-induced structural transition of BSA at pH2 and at concentrations of >0.75%, which involves the exposure of its hydrophobic core to the solution. We confirm our results with the common tryptophan emission method, and show that the use of photoacids can result in a much more sensitive tool. We also show that common fluorescent probes and the CD methodologies have fundamental restrictions that limit their use in a concentration-dependent study. The use of photoacids is facile and requires only a fluorospectrometer (and preferably, but not mandatorily, a time-resolution emission system). The photoacid can be either non-covalently (as in this study) or covalently attached to the molecule, and can be readily employed to follow the local environment of numerous (bio-)systems.
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Affiliation(s)
- Nadav Amdursky
- Departments of Materials and Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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182
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Palamini M, Canciani A, Forneris F. Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Front Mol Biosci 2016; 3:47. [PMID: 27668215 PMCID: PMC5016524 DOI: 10.3389/fmolb.2016.00047] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/22/2016] [Indexed: 12/29/2022] Open
Abstract
Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.
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Affiliation(s)
| | | | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of PaviaPavia, Italy
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183
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Román-Morales E, López-Alfonzo E, Pietri R, López-Garriga J. Sulfmyoglobin Conformational Change: A Role in the Decrease of Oxy-Myoglobin Functionality. Biochem Biophys Rep 2016; 7:386-393. [PMID: 28138567 PMCID: PMC5269605 DOI: 10.1016/j.bbrep.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 12/27/2022] Open
Abstract
This work is focused at understanding the interaction of H2S with Myoglobin (Mb), in particular the Sulfmyoglobin (SMb) product, whose physiological role is controversial and not well understood. The scattering curves, Guinier, Kratky, Porod and P(r) plots were analyzed for oxy-Mb and oxy-Hemoglobin I (oxyHbI) in the absence and presence of H2S, using Small and Wide Angle X-ray Scattering (SAXS/WAXS) technique. Three dimensional models were also generated from the SAXS/WAXS data. The results show that SMb formation, produced by oxyMb and H2S interaction, induces a change in the protein conformation where its envelope has a very small cleft and the protein is more flexible, less rigid and compact. Based on the direct relationship between Mb's structural conformation and its functionality, we suggest that the conformational change observed upon SMb formation plays a contribution to the protein decrease in O2 affinity and, therefore, on its functionality.
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Affiliation(s)
| | | | | | - Juan López-Garriga
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, PO BOX 9019, Mayagüez, Puerto Rico 00681‐9019
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184
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Di Carlo MG, Vetri V, Buscarino G, Leone M, Vestergaard B, Foderà V. Trifluoroethanol modulates α-synuclein amyloid-like aggregate formation, stability and dissolution. Biophys Chem 2016; 216:23-30. [DOI: 10.1016/j.bpc.2016.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/13/2016] [Accepted: 06/20/2016] [Indexed: 01/05/2023]
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185
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Barber-Zucker S, Uebe R, Davidov G, Navon Y, Sherf D, Chill JH, Kass I, Bitton R, Schüler D, Zarivach R. Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance. Sci Rep 2016; 6:31933. [PMID: 27550551 PMCID: PMC4994047 DOI: 10.1038/srep31933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/29/2016] [Indexed: 11/08/2022] Open
Abstract
Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins' proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - René Uebe
- Department of Microbiology, University of Bayreuth, Bayreuth, 95447, Germany
| | - Geula Davidov
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Yotam Navon
- Department of Chemical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Dror Sherf
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Jordan H. Chill
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Itamar Kass
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ronit Bitton
- Department of Chemical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, 95447, Germany
| | - Raz Zarivach
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
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186
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Díaz-Ayala R, Moya-Rodríguez A, Pietri R, Cadilla CL, López-Garriga J. Molecular Cloning and Characterization of a (Lys)6-Tagged Sulfide-Reactive Hemoglobin I from Lucina pectinata. Mol Biotechnol 2016; 57:1050-62. [PMID: 26482241 DOI: 10.1007/s12033-015-9896-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A poly-Lys tag was fused to the Lucina pectinata hemoglobin I (HbI) coding sequence and purified using an efficient and fast process. HbI is a hemeprotein that binds hydrogen sulfide (H2S) with high affinity and it has been used to understand physiologically relevant reactions of this signaling molecule. The (Lys)6-tagged rHbI construct was expressed in E. coli and purified by immobilization on a cation exchange matrix, followed by size-exclusion chromatography. The identity, structure, and function of the (Lys)6-tagged rHbI were assessed by mass spectrometry, small and wide X-ray scattering, optical spectroscopy, and kinetic analysis. The scattering and spectroscopic results showed that the (Lys)6-tagged rHbI is structurally and functionally analogous to the native protein as well as to the (His)6-tagged rHbI. Kinetics studies with H2S indicated that the association (k on) and dissociation (k off) rate constants were 1.4 × 10(5)/M/s and 0.1 × 10(-3)/s, respectively. This results confirmed that the (Lys)6-tagged rHbI binds H2S with the same high affinity as its homologue.
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187
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Dimer conformation of soluble PECAM-1, an endothelial marker. Int J Biochem Cell Biol 2016; 77:102-108. [DOI: 10.1016/j.biocel.2016.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 02/26/2016] [Accepted: 06/02/2016] [Indexed: 11/18/2022]
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188
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Schindler C, de Vries S, Sasse A, Zacharias M. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Structure 2016; 24:1387-1397. [DOI: 10.1016/j.str.2016.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
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189
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Tong D, Yang S, Lu L. Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures. J Appl Crystallogr 2016; 49:1148-1161. [PMID: 28074088 PMCID: PMC5223287 DOI: 10.1107/s1600576716007962] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/15/2016] [Indexed: 02/04/2023] Open
Abstract
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.
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Affiliation(s)
- Dudu Tong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, Case Western Reserve University, 10900 Euclid Avenue, BRB 929, Cleveland, OH 44106-4988, USA
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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190
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Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C. The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 2016; 283:3134-54. [PMID: 27390177 DOI: 10.1111/febs.13801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions. DATABASE Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.
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Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | | | - Angela Cattaneo
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
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191
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Li KB, Li N, Zang Y, Chen GR, Li J, James TD, He XP, Tian H. Foldable glycoprobes capable of fluorogenic crosslinking of biomacromolecules. Chem Sci 2016; 7:6325-6329. [PMID: 28567244 PMCID: PMC5450440 DOI: 10.1039/c6sc02366e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/11/2016] [Indexed: 01/10/2023] Open
Abstract
We demonstrate a foldable, fluorogenic glycoprobe that can recognize and simultaneously crosslink a receptor protein to form unique supramolecular bio-ensembles.
Small-molecular probes capable of monitoring and interfering with the activity of biomacromolecules – such as polysaccharides, nucleotides and proteins – are of paramount importance to the advancement of life science. However, such probes that can detect and simultaneously modulate the construction of biomacromolecules are elusive. Here we report a fluorogenic, foldable glycoprobe that can recognize and assemble a protein receptor in a synchronous fashion. The glycoprobe synthesized by introducing a glycoligand (for protein recognition) to a bola-type bis-fluorophore conjugate shows a “self-shielded” fluorescence in the folded state. Association with a receptor protein rapidly unfolds the probe, releasing a fluorophore capable of crosslinking the proteins – as determined using small-angle X-ray scattering – thereby producing a unique fluorescent supramolecular construct. We have demonstrated the use of the foldable glycoprobe in order to track the endocytic cycle of a transmembrane receptor.
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Affiliation(s)
- Kai-Bin Li
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals , School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Meilong Rd. , Shanghai 200237 , PR China .
| | - Na Li
- National Center for Protein Science Shanghai , Shanghai Institutes of Biological Sciences , Chinese Academy of Sciences , Shanghai 200031 , PR China
| | - Yi Zang
- National Center for Drug Screening , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 189 Guo Shoujing Rd. , Shanghai 201203 , PR China .
| | - Guo-Rong Chen
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals , School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Meilong Rd. , Shanghai 200237 , PR China .
| | - Jia Li
- National Center for Drug Screening , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 189 Guo Shoujing Rd. , Shanghai 201203 , PR China .
| | - Tony D James
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals , School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Meilong Rd. , Shanghai 200237 , PR China .
| | - He Tian
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals , School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Meilong Rd. , Shanghai 200237 , PR China .
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192
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Gonçalves KM, Junior II, Papadimitriou V, Zoumpanioti M, Leal ICR, de Souza ROMA, Cordeiro Y, Xenakis A. Nanoencapsulated Lecitase Ultra and Thermomyces lanuginosus Lipase, a Comparative Structural Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6746-6756. [PMID: 27291999 DOI: 10.1021/acs.langmuir.6b00826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Two commercially available and widely used enzymes, the parent Thermomyces lanuginosus lipase (TLL) and the shuffled phospholipase A1 Lecitase (Lecitase Ultra), were encapsulated in AOT/isooctane reverse micelles and evaluated regarding their structure and activity. Preparations were also tested as effective biocatalysts. Small-angle X-ray scattering (SAXS), electronic paramagnetic resonance (EPR), and fluorescence spectroscopy were the techniques applied to assess the effects of enzyme incorporation to a reverse micellar nanostructure. SAXS analysis showed that the radius of gyration (Rg) changed from 16 to 38 Å, as the water content (w0) increased. Elongated shapes were more commonly observed than spherical shapes after enzyme encapsulation. EPR studies indicated that enzymes do not participate in the interface, being located in the aqueous center. Fluorescence energy transfer showed that TLL is located in the water core, whereas Lecitase Ultra is closer to the interface. Enzymatic activity toward a standard esterification reaction endured after the enzyme was incorporated into the micelles. The activity of TLL for systems with w0 15 showed the highest conversion yield, 38% in 2 h, while the system with w0 10 showed the highest initial velocity, 0.43 μM/min. This last system had a Rg of 19.3 Å, similar to that of the TLL monomer. Lecitase Ultra showed the highest conversion yields in systems with w0 10, 55% in 2 h. However, the initial rate was much lower than that of TLL, suggesting less affinity for the substrates, which is expected since Lecitase Ultra is a phospholipase. In summary, we here used several spectroscopic and scattering techniques to reveal the shape and stability of TTL and Lecitase Ultra encapsulated systems, which allowed the selection of w0 values to provide optimized enzymatic activity.
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Affiliation(s)
- Karen M Gonçalves
- Faculty of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro 21941-902, Brazil
| | - Ivaldo I Junior
- Biocatalysis and Organic Synthesis Group, Chemistry Institute, Federal University of Rio de Janeiro , Rio de Janeiro 21941-909, Brazil
- Department of Biochemical Engineering, School of Chemistry, Federal University of Rio de Janeiro , Rio de Janeiro 21941-909, Brazil
| | - Vassiliki Papadimitriou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens 116 35, Greece
| | - Maria Zoumpanioti
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens 116 35, Greece
| | - Ivana C R Leal
- Faculty of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro 21941-902, Brazil
| | - Rodrigo O M A de Souza
- Biocatalysis and Organic Synthesis Group, Chemistry Institute, Federal University of Rio de Janeiro , Rio de Janeiro 21941-909, Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro 21941-902, Brazil
| | - Aristotelis Xenakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens 116 35, Greece
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193
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Young BH, Caldwell TA, McKenzie AM, Kokhan O, Berndsen CE. Characterization of the structure and catalytic activity of Legionella pneumophila VipF. Proteins 2016; 84:1422-30. [PMID: 27315603 DOI: 10.1002/prot.25087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 11/05/2022]
Abstract
The pathogenic bacteria Legionella pneumophila is known to cause Legionnaires' Disease, a severe pneumonia that can be fatal to immunocompromised individuals and the elderly. Shohdy et al. identified the L. pneumophila vacuole sorting inhibitory protein VipF as a putative N-acetyltransferase based on sequence homology. We have characterized the basic structural and functional properties of VipF to confirm this original functional assignment. Sequence conservation analysis indicates two putative CoA-binding regions within VipF. Homology modeling and small angle X-ray scattering suggest a monomeric, dual-domain structure joined by a flexible linker. Each domain contains the characteristic beta-splay motif found in many acetyltransferases, suggesting that VipF may contain two active sites. Docking experiments suggest reasonable acetyl-CoA binding locations within each beta-splay motif. Broad substrate screening indicated that VipF is capable of acetylating chloramphenicol and both domains are catalytically active. Given that chloramphenicol is not known to be N-acetylated, this is a surprising finding suggesting that VipF is capable of O-acetyltransferase activity. Proteins 2016; 84:1422-1430. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Byron H Young
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Tracy A Caldwell
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Aidan M McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807.
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194
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Peng J, Zhang Z. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations. Sci Rep 2016; 6:29360. [PMID: 27377017 PMCID: PMC4932515 DOI: 10.1038/srep29360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022] Open
Abstract
Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.
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Affiliation(s)
- Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
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195
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A Structure-free Method for Quantifying Conformational Flexibility in proteins. Sci Rep 2016; 6:29040. [PMID: 27358108 PMCID: PMC4928179 DOI: 10.1038/srep29040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022] Open
Abstract
All proteins sample a range of conformations at physiologic temperatures and this inherent flexibility enables them to carry out their prescribed functions. A comprehensive understanding of protein function therefore entails a characterization of protein flexibility. Here we describe a novel approach for quantifying a protein’s flexibility in solution using small-angle X-ray scattering (SAXS) data. The method calculates an effective entropy that quantifies the diversity of radii of gyration that a protein can adopt in solution and does not require the explicit generation of structural ensembles to garner insights into protein flexibility. Application of this structure-free approach to over 200 experimental datasets demonstrates that the methodology can quantify a protein’s disorder as well as the effects of ligand binding on protein flexibility. Such quantitative descriptions of protein flexibility form the basis of a rigorous taxonomy for the description and classification of protein structure.
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196
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Bhagawati M, Rubashkin MG, Lee JP, Ananthanarayanan B, Weaver VM, Kumar S. Site-Specific Modulation of Charge Controls the Structure and Stimulus Responsiveness of Intrinsically Disordered Peptide Brushes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5990-5996. [PMID: 27203736 PMCID: PMC5343758 DOI: 10.1021/acs.langmuir.6b01099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important and emerging class of materials for tailoring biointerfaces. While the importance of chain charge and resultant electrostatic interactions in controlling conformational properties of IDPs is beginning to be explored through in silico approaches, there is a dearth of experimental studies motivated toward a systematic study of these effects. In an effort to explore this relationship, we measured the conformations of two peptides derived from the intrinsically disordered neurofilament (NF) side arm domain: one depicting the wild-type sequence with four lysine-serine-proline repeats (KSP peptide) and another in which the serine residues were replaced with aspartates (KDP peptide), a strategy sometimes used to mimic phosphorylation. Using a variety of biophysical measurements including a novel application of scanning angle interference microscopy, we demonstrate that the KDP peptide assumes comparatively more expanded conformations in solution and forms significantly thicker brushes when immobilized on planar surfaces at high densities. In both settings, the peptides respond to changes in ambient ionic strength, with each peptide showing distinct stimulus-responsive characteristics. While the KDP peptide undergoes compaction with increasing ionic strength as would be expected for a polyampholyte, the KSP peptide shows biphasic behavior, with an initial compaction followed by an expanded state at a higher ionic strength. Together these results support the notion that modulation of charge on IDPs can regulate conformational and interfacial properties.
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Affiliation(s)
- Maniraj Bhagawati
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Matt G. Rubashkin
- Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, California 94143, United States
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jessica P. Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | | | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, California 94143, United States
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Sanjay Kumar
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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197
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Berneking L, Schnapp M, Rumm A, Trasak C, Ruckdeschel K, Alawi M, Grundhoff A, Kikhney AG, Koch-Nolte F, Buck F, Perbandt M, Betzel C, Svergun DI, Hentschke M, Aepfelbacher M. Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells. PLoS Pathog 2016; 12:e1005660. [PMID: 27300509 PMCID: PMC4907486 DOI: 10.1371/journal.ppat.1005660] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Yersinia outer protein M (YopM) is a crucial immunosuppressive effector of the plaque agent Yersinia pestis and other pathogenic Yersinia species. YopM enters the nucleus of host cells but neither the mechanisms governing its nucleocytoplasmic shuttling nor its intranuclear activities are known. Here we identify the DEAD-box helicase 3 (DDX3) as a novel interaction partner of Y. enterocolitica YopM and present the three-dimensional structure of a YopM:DDX3 complex. Knockdown of DDX3 or inhibition of the exportin chromosomal maintenance 1 (CRM1) increased the nuclear level of YopM suggesting that YopM exploits DDX3 to exit the nucleus via the CRM1 export pathway. Increased nuclear YopM levels caused enhanced phosphorylation of Ribosomal S6 Kinase 1 (RSK1) in the nucleus. In Y. enterocolitica infected primary human macrophages YopM increased the level of Interleukin-10 (IL-10) mRNA and this effect required interaction of YopM with RSK and was enhanced by blocking YopM's nuclear export. We propose that the DDX3/CRM1 mediated nucleocytoplasmic shuttling of YopM determines the extent of phosphorylation of RSK in the nucleus to control transcription of immunosuppressive cytokines.
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Affiliation(s)
- Laura Berneking
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marie Schnapp
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Andreas Rumm
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Claudia Trasak
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Klaus Ruckdeschel
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | | | - Friedrich Buck
- Institute of Clinical Chemistry, University Medical Center, Hamburg, Germany
| | - Markus Perbandt
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Laboratory of Structural Biology of Infection and Inflammation, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Laboratory of Structural Biology of Infection and Inflammation, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Moritz Hentschke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- * E-mail:
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198
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Björling A, Niebling S, Marcellini M, van der Spoel D, Westenhoff S. Deciphering solution scattering data with experimentally guided molecular dynamics simulations. J Chem Theory Comput 2016; 11:780-7. [PMID: 25688181 PMCID: PMC4325560 DOI: 10.1021/ct5009735] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 01/26/2023]
Abstract
![]()
Time-resolved
X-ray solution scattering is an increasingly popular
method to measure conformational changes in proteins. Extracting structural
information from the resulting difference X-ray scattering data is
a daunting task. We present a method in which the limited but precious
information encoded in such scattering curves is combined with the
chemical knowledge of molecular force fields. The molecule of interest
is then refined toward experimental data using molecular dynamics
simulation. Therefore, the energy landscape is biased toward conformations
that agree with experimental data. We describe and verify the method,
and we provide an implementation in GROMACS.
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Affiliation(s)
- Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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199
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Dadinova LA, Rodina EV, Vorobyeva NN, Kurilova SA, Nazarova TI, Shtykova EV. Structural investigations of E. Coli dihydrolipoamide dehydrogenase in solution: Small-angle X-ray scattering and molecular docking. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516030093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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200
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Borges JC, Seraphim TV, Dores-Silva PR, Barbosa LRS. A review of multi-domain and flexible molecular chaperones studies by small-angle X-ray scattering. Biophys Rev 2016; 8:107-120. [PMID: 28510050 PMCID: PMC5425780 DOI: 10.1007/s12551-016-0194-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Intrinsic flexibility is closely related to protein function, and a plethora of important regulatory proteins have been found to be flexible, multi-domain or even intrinsically disordered. On the one hand, understanding such systems depends on how these proteins behave in solution. On the other, small-angle X-ray scattering (SAXS) is a technique that fulfills the requirements to study protein structure and dynamics relatively quickly with few experimental limitations. Molecular chaperones from Hsp70 and Hsp90 families are multi-domain proteins containing flexible and/or disordered regions that play central roles in cellular proteostasis. Here, we review the structure and function of these proteins by SAXS. Our general approach includes the use of SAXS data to determine size and shape parameters, as well as protein shape reconstruction and their validation by using accessory biophysical tools. Some remarkable examples are presented that exemplify the potential of the SAXS technique. Protein structure can be determined in solution even at limiting protein concentrations (for example, human mortalin, a mitochondrial Hsp70 chaperone). The protein organization, flexibility and function (for example, the J-protein co-chaperones), oligomeric status, domain organization, and flexibility (for the Hsp90 chaperone and the Hip and Hep1 co-chaperones) may also be determined. Lastly, the shape, structural conservation, and protein dynamics (for the Hsp90 chaperone and both p23 and Aha1 co-chaperones) may be studied by SAXS. We believe this review will enhance the application of the SAXS technique to the study of the molecular chaperones.
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Affiliation(s)
- Júlio C Borges
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil.
| | - Thiago V Seraphim
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Paulo R Dores-Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
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