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Ural MS, Joseph JM, Wien F, Li X, Tran MA, Taverna M, Smadja C, Gref R. A comprehensive investigation of the interactions of human serum albumin with polymeric and hybrid nanoparticles. Drug Deliv Transl Res 2024; 14:2188-2202. [PMID: 38578378 DOI: 10.1007/s13346-024-01578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Nanoparticles (NPs) engineered as drug delivery systems continue to make breakthroughs as they offer numerous advantages over free therapeutics. However, the poor understanding of the interplay between the NPs and biomolecules, especially blood proteins, obstructs NP translation to clinics. Nano-bio interactions determine the NPs' in vivo fate, efficacy and immunotoxicity, potentially altering protein function. To fulfill the growing need to investigate nano-bio interactions, this study provides a systematic understanding of two key aspects: (i) protein corona (PC) formation and (ii) NP-induced modifications on protein's structure and stability. A methodology was developed by combining orthogonal techniques to analyze both quantitative and qualitative aspects of nano-bio interactions, using human serum albumin (HSA) as a model protein. Protein quantification via liquid chromatography-mass spectrometry, and capillary zone electrophoresis (CZE) clarified adsorbed protein quantity and stability. CZE further unveiled qualitative insights into HSA forms (native, glycated HSA and cysteinylated), while synchrotron radiation circular dichroism enabled analyzing HSA's secondary structure and thermal stability. Comparative investigations of NP cores (organic vs. hybrid), and shells (with or without polyethylene glycol (PEG)) revealed pivotal factors influencing nano-bio interactions. Polymeric NPs based on poly(lactic-co-glycolic acid) (PLGA) and hybrid NPs based on metal-organic frameworks (nanoMOFs) presented distinct HSA adsorption profiles. PLGA NPs had protein-repelling properties while inducing structural modifications on HSA. In contrast, HSA exhibited a high affinity for nanoMOFs forming a PC altering thereby the protein structure. A shielding effect was gained through PEGylation for both types of NPs, avoiding the PC formation as well as the alteration of unbound HSA structure.
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Affiliation(s)
- Merve Seray Ural
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Joice Maria Joseph
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Frank Wien
- , Synchrotron Soleil, 91190, Saint-Aubin, France
| | - Xue Li
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
| | - My-An Tran
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
| | - Myriam Taverna
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Claire Smadja
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France.
| | - Ruxandra Gref
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France.
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2
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Osman R, Bossu M, Dauvillée D, Spriet C, Liu C, Zeeman SC, D'Hulst C, Bompard C. LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis. PLANT PHYSIOLOGY 2024; 195:1851-1865. [PMID: 38573555 DOI: 10.1093/plphys/kiae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.
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Affiliation(s)
- Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mélanie Bossu
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - David Dauvillée
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille F-59000, France
| | - Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Christophe D'Hulst
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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3
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Liu C, Pfister B, Osman R, Ritter M, Heutinck A, Sharma M, Eicke S, Fischer-Stettler M, Seung D, Bompard C, Abt MR, Zeeman SC. LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis. SCIENCE ADVANCES 2023; 9:eadg7448. [PMID: 37235646 DOI: 10.1126/sciadv.adg7448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.
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Affiliation(s)
- Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Barbara Pfister
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maximilian Ritter
- Institute for Building Materials, ETH Zurich, Stefano-Franscini-Platz 3, 8093 Zurich, Switzerland
| | - Arvid Heutinck
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | - David Seung
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Melanie R Abt
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
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4
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Milogrodzka I, Nguyen Pham DT, Sama GR, Samadian H, Zhai J, de Campo L, Kirby NM, Scott TF, Banaszak Holl MM, van 't Hag L. Effect of Cholesterol on Biomimetic Membrane Curvature and Coronavirus Fusion Peptide Encapsulation. ACS NANO 2023; 17:8598-8612. [PMID: 37078604 DOI: 10.1021/acsnano.3c01095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Biomimetic cubic phases can be used for protein encapsulation in a variety of applications such as biosensors and drug delivery. Cubic phases with a high concentration of cholesterol and phospholipids were obtained herein. It is shown that the cubic phase structure can be maintained with a higher concentration of biomimetic membrane additives than has been reported previously. Opposing effects on the curvature of the membrane were observed upon the addition of phospholipids and cholesterol. Furthermore, the coronavirus fusion peptide significantly increased the negative curvature of the biomimetic membrane with cholesterol. We show that the viral fusion peptide can undergo structural changes leading to the formation of hydrophobic α-helices that insert into the lipid bilayer. This is of high importance, as a fusion peptide that induces increased negative curvature as shown by the formation of inverse hexagonal phases allows for greater contact area between two membranes, which is required for viral fusion to occur. The cytotoxicity assay showed that the toxicity toward HeLa cells was dramatically decreased when the cholesterol or peptide level in the nanoparticles increased. This suggests that the addition of cholesterol can improve the biocompatibility of the cubic phase nanoparticles, making them safer for use in biomedical applications. As the results, this work improves the potential for the biomedical end-use applications of the nonlamellar lipid nanoparticles and shows the need of systematic formulation studies due to the complex interplay of all components.
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Affiliation(s)
- Izabela Milogrodzka
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Duy Tue Nguyen Pham
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gopal R Sama
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Hajar Samadian
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Liliana de Campo
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, NSW 2234, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Timothy F Scott
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Mark M Banaszak Holl
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Mechanical and Materials Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Leonie van 't Hag
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
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5
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Hajdu B, Hunyadi-Gulyás É, Kato K, Kawaguchi A, Nagata K, Gyurcsik B. Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. J Biol Inorg Chem 2023; 28:301-315. [PMID: 36820987 PMCID: PMC10036435 DOI: 10.1007/s00775-023-01988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site = - (23.5 - 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ'pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ'pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ' unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.
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Affiliation(s)
- Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary.
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6
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Nguyen DD, Jones NC, Hoffmann SV, Spanget-Larsen J. Near and vacuum UV polarization spectroscopy of 1,4-distyrylbenzene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:122019. [PMID: 36308827 DOI: 10.1016/j.saa.2022.122019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The UV absorbance bands of 1,4-distyrylbenzene (1,4-Bis[(E)-2-phenylethenyl]benzene, DSB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The observed polarization data provide information on the transition moment directions of the observed spectral features. The investigation covers the range 15,000-58,000 cm-1 (667-172 nm), thereby providing new information on the transitions of DSB in the vacuum UV region. The observed spectrum is characterized by four main band systems centered at 27,600, 41,000, 49,800, and 57,500 cm-1 (362, 244, 201, and 174 nm). In general, the observed bands and their polarization directions are well predicted by the results of quantum chemical calculations using Time-Dependent Density Functional Theory (TD-DFT) with the functional CAM-B3LYP, and with the semiempirical all-valence-electrons method LCOAO.
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Affiliation(s)
- Duy Duc Nguyen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Søren V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Jens Spanget-Larsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark.
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7
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Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
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8
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Garcia AD, Topin J, Bocková J, Jones NC, Hoffmann SV, Meinert C. Chiroptical activity of gas-phase propylene oxide predicting the handedness of interstellar circular polarization in the presolar nebula. SCIENCE ADVANCES 2022; 8:eadd4614. [PMID: 36399555 PMCID: PMC9674286 DOI: 10.1126/sciadv.add4614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Propylene oxide, the first chiral molecule recently detected in the interstellar medium, has once again raised the question whether biomolecular chirality might have cosmic origins. However, accurate chiroptical properties of propylene oxide in the ultraviolet spectral range necessary to suggest possible asymmetric synthetic routes in the gas phase are scarce. Here, we report on the first experimental measurements of the anisotropy spectra of gas-phase propylene oxide in the vacuum ultraviolet spectral range. Our experimental results provide novel insights into the handedness of interstellar circular polarization at the dawn of molecular evolution of our star- and planet-forming region. Besides the fundamental importance of this new investigation for understanding the origin and evolution of homochirality on Earth, our high-resolution experimental electronic circular dichroism data will inspire new efforts in quantum computational spectroscopy.
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Affiliation(s)
- Adrien D. Garcia
- Institut de Chimie de Nice, Université Côte d’Azur, UMR 7272 CNRS, Nice 06108, France
| | - Jérémie Topin
- Institut de Chimie de Nice, Université Côte d’Azur, UMR 7272 CNRS, Nice 06108, France
| | - Jana Bocková
- Institut de Chimie de Nice, Université Côte d’Azur, UMR 7272 CNRS, Nice 06108, France
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | - Søren V. Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | - Cornelia Meinert
- Institut de Chimie de Nice, Université Côte d’Azur, UMR 7272 CNRS, Nice 06108, France
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9
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Balogh RK, Gyurcsik B, Jensen M, Thulstrup PW, Köster U, Christensen NJ, Jensen ML, Hunyadi-Gulyás É, Hemmingsen L, Jancso A. Tying up a loose end: On the role of the C-terminal CCHHRAG fragment of the metalloregulator CueR. Chembiochem 2022; 23:e202200290. [PMID: 35714117 PMCID: PMC9542689 DOI: 10.1002/cbic.202200290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 11/07/2022]
Abstract
The transcriptional regulator CueR is activated by the binding of CuI, AgI, or AuI to two cysteinates in a near‐linear fashion. The C‐terminal CCHHRAG sequence in Escherichia coli CueR present potential additional metal binding ligands and here we explore the effect of deleting this fragment on the binding of AgI to CueR. CD spectroscopic and ESI‐MS data indicate that the high AgI‐binding affinity of WT‐CueR is significantly reduced in Δ7C‐CueR.[111 Ag PAC spectroscopy demonstrates that the WT‐CueR metal site structure (AgS2) is conserved, but less populated in the truncated variant. Thus, the function of the C‐terminal fragment may be to stabilize the two‐coordinate metal site for cognate monovalent metal ions. In a broader perspective this is an example of residues beyond the second coordination sphere affecting metal site physicochemical properties while leaving the structure unperturbed.
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Affiliation(s)
- Ria K Balogh
- University of Szeged: Szegedi Tudomanyegyetem, Department of Inorganic and Analytical Chemistry, HUNGARY
| | - Béla Gyurcsik
- University of Szeged: Szegedi Tudomanyegyetem, Department of Inorganic and Analytical Chemistry, HUNGARY
| | - Mikael Jensen
- Technical University of Denmark: Danmarks Tekniske Universitet, Hevesy Laboratory, Center for Nuclear Technologies, DENMARK
| | - Peter W Thulstrup
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | - Ulli Köster
- Institut Laue-Langevin, Institut Laue-Langevin, FRANCE
| | - Niels Johan Christensen
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, Faculty of Science, DENMARK
| | - Marianne L Jensen
- Niels Bohr Instituttet: Kobenhavns Universitet Niels Bohr Instituttet, Niels Bohr Institute, DENMARK
| | - Éva Hunyadi-Gulyás
- Biological Research Centre, Szeged, Laboratory of Proteomics Research, HUNGARY
| | - Lars Hemmingsen
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | - Attila Jancso
- University of Szeged, Department of Inorganic and Analytical Chemistry, Dóm tér 7., 6720, Szeged, HUNGARY
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10
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Hartmann S, Ling M, Dreyer LSA, Zipori A, Finster K, Grawe S, Jensen LZ, Borck S, Reicher N, Drace T, Niedermeier D, Jones NC, Hoffmann SV, Wex H, Rudich Y, Boesen T, Šantl-Temkiv T. Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity. Front Microbiol 2022; 13:872306. [PMID: 35783412 PMCID: PMC9247515 DOI: 10.3389/fmicb.2022.872306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the β-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.
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Affiliation(s)
| | - Meilee Ling
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Lasse S. A. Dreyer
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Assaf Zipori
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kai Finster
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
| | - Sarah Grawe
- Institute for Tropospheric Research, Leipzig, Germany
| | - Lasse Z. Jensen
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Stella Borck
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Taner Drace
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | | | - Nykola C. Jones
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Søren V. Hoffmann
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Heike Wex
- Institute for Tropospheric Research, Leipzig, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center and Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Thomas Boesen,
| | - Tina Šantl-Temkiv
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- *Correspondence: Tina Šantl-Temkiv,
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11
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Synchrotron Radiation Circular Dichroism, a New Tool to Probe Interactions between Nucleic Acids Involved in the Control of ColE1-Type Plasmid Replication. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Hfq is a bacterial master regulator which promotes the pairing of nucleic acids. Due to the high molecular weight of the complexes formed between nucleic acids and the amyloid form of the protein, it is difficult to analyze solely by a gel shift assay the complexes formed, as they all migrate at the same position in the gel. In addition, precise kinetics measurements are not possible using a gel shift assay. Here, we used a synchrotron-based biophysical approach, synchrotron radiation circular dichroism (SRCD), to probe the interaction of the Escherichia coli Hfq C-terminal amyloid region with nucleic acids involved in the control of ColE1-like plasmid replication. We observed that this C-terminal region of Hfq has an unexpected and significant effect on the annealing of nucleic acids involved in this process and, more importantly, on their alignment. Functional consequences of this newly discovered property of the Hfq amyloid region are discussed in terms of the biological significance of Hfq in the ColE1-type plasmid replication process and antibiotic resistance.
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12
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Sharma A, Khamar D, Cullen S, Hayden A, Hughes H. Innovative Drying Technologies for Biopharmaceuticals. Int J Pharm 2021; 609:121115. [PMID: 34547393 DOI: 10.1016/j.ijpharm.2021.121115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 01/30/2023]
Abstract
In the past two decades, biopharmaceuticals have been a breakthrough in improving the quality of lives of patients with various cancers, autoimmune, genetic disorders etc. With the growing demand of biopharmaceuticals, the need for reducing manufacturing costs is essential without compromising on the safety, quality, and efficacy of products. Batch Freeze-drying is the primary commercial means of manufacturing solid biopharmaceuticals. However, Freeze-drying is an economically unfriendly means of production with long production cycles, high energy consumption and heavy capital investment, resulting in high overall costs. This review compiles some potential, innovative drying technologies that have not gained popularity for manufacturing parenteral biopharmaceuticals. Some of these technologies such as Spin-freeze-drying, Spray-drying, Lynfinity® Technology etc. offer a paradigm shift towards continuous manufacturing, whereas PRINT® Technology and MicroglassificationTM allow controlled dry particle characteristics. Also, some of these drying technologies can be easily scaled-up with reduced requirement for different validation processes. The inclusion of Process Analytical Technology (PAT) and offline characterization techniques in tandem can provide additional information on the Critical Process Parameters (CPPs) and Critical Quality Attributes (CQAs) during biopharmaceutical processing. These processing technologies can be envisaged to increase the manufacturing capacity for biopharmaceutical products at reduced costs.
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Affiliation(s)
- Ashutosh Sharma
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland.
| | - Dikshitkumar Khamar
- Sanofi, Manufacturing Science, Analytics and Technology (MSAT), IDA Industrial Park, Waterford X91TP27, Ireland
| | - Sean Cullen
- Gilead Sciences, Commercial Manufacturing, IDA Business & Technology Park, Carrigtwohill, Co. Cork T45DP77, Ireland
| | - Ambrose Hayden
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
| | - Helen Hughes
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
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13
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Théron L, Bonifacie A, Delabre J, Sayd T, Aubry L, Gatellier P, Ravel C, Chambon C, Astruc T, Rouel J, Santé-Lhoutellier V, Réfrégiers M, Wien F. Investigation by Synchrotron Radiation Circular Dichroism of the Secondary Structure Evolution of Pepsin under Oxidative Environment. Foods 2021; 10:foods10050998. [PMID: 34063224 PMCID: PMC8147470 DOI: 10.3390/foods10050998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Food processing affects the structure and chemical state of proteins. In particular, protein oxidation occurs and may impair protein properties. These chemical reactions initiated during processing can develop during digestion. Indeed, the physicochemical conditions of the stomach (oxygen pressure, low pH) favor oxidation. In that respect, digestive proteases may be affected as well. Yet, very little is known about the link between endogenous oxidation of digestive enzymes, their potential denaturation, and, therefore, food protein digestibility. Thus, the objective of this study is to understand how oxidative chemical processes will impact the pepsin secondary structure and its hydrolytic activity. The folding and unfolding kinetics of pepsin under oxidative conditions was determined using Synchrotron Radiation Circular Dichroism. SRCD gave us the possibility to monitor the rapid kinetics of protein folding and unfolding in real-time, giving highly resolved spectral data. The proteolytic activity of control and oxidized pepsin was investigated by MALDI-TOF mass spectrometry on a meat protein model, the creatine kinase. MALDI-TOF MS allowed a rapid evaluation of the proteolytic activity through peptide fingerprint. This study opens up new perspectives by shifting the digestion paradigm taking into account the gastric digestive enzyme and its substrate.
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Affiliation(s)
- Laetitia Théron
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
- Correspondence:
| | - Aline Bonifacie
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Jérémy Delabre
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), Plateforme D’exploration du Métabolisme Composante Protéomique (PFEMcp), F-63122 Saint Genès-Champanelle, France; (J.D.); (C.C.)
| | - Thierry Sayd
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Laurent Aubry
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Philippe Gatellier
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Christine Ravel
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Christophe Chambon
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), Plateforme D’exploration du Métabolisme Composante Protéomique (PFEMcp), F-63122 Saint Genès-Champanelle, France; (J.D.); (C.C.)
| | - Thierry Astruc
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Jacques Rouel
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Véronique Santé-Lhoutellier
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Matthieu Réfrégiers
- DISCO Beamline, Synchrotron SOLEIL, F-91192 Gif-sur-Yvette, France; (M.R.); (F.W.)
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, F-45071 Orléans, France
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, F-91192 Gif-sur-Yvette, France; (M.R.); (F.W.)
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14
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Evans AC, Petit AS, Guillen SG, Neukirch AJ, Hoffmann SV, Jones NC. Chiroptical characterization tools for asymmetric small molecules - experimental and computational approaches for electronic circular dichroism (ECD) and anisotropy spectroscopy. RSC Adv 2021; 11:1635-1643. [PMID: 35424126 PMCID: PMC8693638 DOI: 10.1039/d0ra06832b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/15/2020] [Indexed: 11/24/2022] Open
Abstract
Synchrotron radiation electronic circular dichroism (SRECD) and anisotropy spectroscopy for both enantiomers of a group of small non-planar chiral molecules are reported here. The experimental SRECD spectra are compared to computational ECD spectra generated using time-dependent density functional theory and a thermal averaging over relevant molecular configurations. The combination of these experimental and computational characterization methodologies for such molecules enables the prediction and understanding of the spectral behavior of other small molecules, in addition to chiroptically characterizing members of the mandelic acid family substructure. Enantiomeric purity of samples can be evaluated in comparison with these spectra and the extent of photolytic enantioinduction can also be predicted using these experimental/calculated SRECD and anisotropy spectra. Experimental and computational electronic circular dichroism spectra are used in conjunction with anisotropy spectra to chiroptically characterize mandelic acid and its derivatives into the vacuum UV.![]()
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Affiliation(s)
- Amanda C Evans
- Biosciences/Theoretical Divisions, Los Alamos National Laboratory P.O. Box 1663, Mailstop E529 Los Alamos NM 87544 USA
| | - Andrew S Petit
- Dept. of Chemistry & Biochemistry, California State University Fullerton 800 N. State College Blvd. Fullerton CA 92831 USA
| | - Steven G Guillen
- Dept. of Chemistry & Biochemistry, California State University Fullerton 800 N. State College Blvd. Fullerton CA 92831 USA
| | - Amanda J Neukirch
- Biosciences/Theoretical Divisions, Los Alamos National Laboratory P.O. Box 1663, Mailstop E529 Los Alamos NM 87544 USA
| | - Søren V Hoffmann
- ISA, Dept. of Physics and Astronomy, Aarhus University Ny Munkegade 120 DK-8000 Aarhus C Denmark
| | - Nykola C Jones
- ISA, Dept. of Physics and Astronomy, Aarhus University Ny Munkegade 120 DK-8000 Aarhus C Denmark
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15
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Kjær C, Jones NC, Stockett MH, Hoffmann SV, Nielsen SB. Circular dichroism, anisotropy and absorption spectroscopy of chlorophyll b in methanol and mixed methanol-water solutions. Phys Chem Chem Phys 2020; 22:26961-26966. [PMID: 33206737 DOI: 10.1039/d0cp03284k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spectroscopic properties of chlorophyll (Chl) strongly depend on interactions with other Chl molecules, a fact that nature exploits in light harvesting by photosynthetic proteins. In solution, complex Chl aggregates are formed that depend not only on the solvent, but also on the detailed preparation procedure. Here we report synchrotron radiation circular dichroism (SRCD) spectra of Chlb in methanol (MeOH) and MeOH/H2O mixtures; in the latter, water molecules assist in the formation of Chl aggregates as Chlb is too hydrophobic to dissolve in water. The magnitude of the most prominent CD signal increases up to 100-fold over time (2-15 hours) when the water content is increased from 0 to 50% in volume, the signal is non-conservative (almost exclusively negative), and sensitive to sample preparation. Three different types of signature CD spectra (Types A to C) are identified depending on preparation, and the change in CD signal over time and with temperature is further analyzed with anisotropy spectroscopy (ratio of simultaneously recorded CD to absorption) and principal component analysis (PCA). We show that CD is clearly superior to pure absorption spectroscopy in identifying structural changes, and anisotropy spectroscopy further increases the sensitivity towards smaller structural changes. PCA on temperature dependent CD data show that depending on preparation, and thus the type of aggregate as revealed by the CD signature, either one (Type A) or two chiral species (Type B) are identified in the spectra, further evidencing the complex nature of Chlb aggregates. Furthermore, the CD signal decreases linearly with volume when a sample of Chlb in MeOH/H2O (i.e., a sample of Chlb aggregates) is diluted, which implies that the aggregation process is irreversible: once aggregates are formed, they largely do not revert back to monomers. However, anisotropy spectroscopy reveals that there are small changes in the aggregates, not directly noticeable in CD and absorption. The work presented here demonstrates, compared to absorption spectroscopy, a clear advantage of CD and anisotropy spectroscopy in studying the complex evolution of Chl samples with time and temperature.
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Affiliation(s)
- Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Denmark.
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16
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Thulstrup PW, Jones NC, Hoffmann SV, Spanget-Larsen J. UV polarisation spectroscopy of 1,4-diethynylbenzene. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1853841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Peter W. Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark
| | - Nykola C. Jones
- Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Søren V. Hoffmann
- Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Jens Spanget-Larsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
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17
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Pantcheva I, Nedzhib A, Antonov L, Gyurcsik B, Dorkov P. New insights into coordination chemistry of Monensin A towards divalent metal ions. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Abd Elhameed HAH, Hajdu B, Jancsó A, Kéri A, Galbács G, Hunyadi-Gulyás É, Gyurcsik B. Modulation of the catalytic activity of a metallonuclease by tagging with oligohistidine. J Inorg Biochem 2020; 206:111013. [PMID: 32088594 DOI: 10.1016/j.jinorgbio.2020.111013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 11/19/2022]
Abstract
Peptide tags are extensively used for affinity purification of proteins. In an optimal case, these tags can be completely removed from the purified protein by a specific protease mediated hydrolysis. However, the interactions of these tags with the target protein may also be utilized for the modulation of the protein function. Here we show that the C-terminal hexahistidine (6 × His) tag can influence the catalytic activity of the nuclease domain of the Colicin E7 metallonuclease (NColE7) used by E. coli to kill competing bacteria under stress conditions. This enzyme non-specifically cleaves the DNA that results in cytotoxicity. We have successfully cloned the genes of NColE7 protein and its R447G mutant into a modified pET-21a DNA vector fusing the affinity tag to the protein upon expression, which would be otherwise not possible in the absence of the gene of the Im7 inhibitory protein. This reflects the inhibitory effect of the 6 × His fusion tag on the nuclease activity, which proved to be a complex process via both coordinative and non-specific steric interactions. The modulatory effect of Zn2+ ion was observed in the catalytic activity experiments. The DNA cleavage ability of the 6 × His tagged enzyme was first enhanced by an increase of metal ion concentration, while high excess of Zn2+ ions caused a lower rate of the DNA cleavage. Modelling of the coordinative effect of the fusion tag by external chelators suggested ternary complex formation instead of removal of the metal ion from the active center.
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Affiliation(s)
- Heba A H Abd Elhameed
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Albert Kéri
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary.
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19
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Jones NC, Nielsen SB, Hoffmann SV. On the delocalization length in RNA single strands of cytosine: how many bases see the light? Phys Chem Chem Phys 2020; 22:2188-2192. [DOI: 10.1039/c9cp05292e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.
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Affiliation(s)
- Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
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20
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Nguyen DD, Jones NC, Hoffmann SV, Spanget-Larsen J. UV synchrotron radiation linear dichroism spectroscopy of the anti-psoriatic drug anthralin. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Anthralin (1,8-dihydroxyanthrone, 1,8-dihydroxy-9(10H)-anthracenone), also known as dithranol and cignolin, is one of the most efficient drugs in the treatment of psoriasis and other skin diseases. The precise mode of biochemical action is not fully understood, but the activity of the drug is increased by the influence of UV radiation. In the present investigation, the UV absorption of anthralin is studied by synchrotron radiation linear dichroism (SRLD) spectroscopy on molecular samples partially aligned in stretched polyethylene, covering the near and vacuum UV regions with wavenumbers ranging from 23,000 to 58,000 cm–1(430–170 nm). The observed polarization spectra are well predicted by quantum chemical calculations using time-dependent density functional theory (TD–DFT). About a dozen spectral features are assigned to computed electronic transitions. The calculations support interpretation of the anomalous fluorescence of anthralin as a result of barrier-less excited state intramolecular proton transfer (ESIPT) to the tautomer 8,9-dihydroxy-1(10H)-anthracenone.
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Affiliation(s)
- Duy Duc Nguyen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Intertek Vietnam Limited, Ho Chi Minh City, Vietnam
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Jens Spanget-Larsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
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21
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Synthesis and characterisation of platinum(IV) polypyridyl complexes with halide axial ligands. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.118964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Abd Elhameed HAH, Hajdu B, Balogh RK, Hermann E, Hunyadi-Gulyás É, Gyurcsik B. Purification of proteins with native terminal sequences using a Ni(II)-cleavable C-terminal hexahistidine affinity tag. Protein Expr Purif 2019; 159:53-59. [PMID: 30905870 DOI: 10.1016/j.pep.2019.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 11/26/2022]
Abstract
The role of the termini of protein sequences is often perturbed by remnant amino acids after the specific protease cleavage of the affinity tags and/or by the amino acids encoded by the plasmid at/around the restriction enzyme sites used to insert the genes. Here we describe a method for affinity purification of a metallonuclease with its precisely determined native termini. First, the gene encoding the target protein is inserted into a newly designed cloning site, which contains two self-eliminating BsmBI restriction enzyme sites. As a consequence, the engineered DNA code of Ni(II)-sensitive Ser-X-His-X motif is fused to the 3'-end of the inserted gene followed by the gene of an affinity tag for protein purification purpose. The C-terminal segment starting from Ser mentioned above is cleaved off from purified protein by a Ni(II)-induced protease-like action. The success of the purification and cleavage was confirmed by gel electrophoresis and mass spectrometry, while structural integrity of the purified protein was checked by circular dichroism spectroscopy. Our new protein expression DNA construct is an advantageous tool for protein purification, when the complete removal of affinity or other tags, without any remaining amino acid residue is essential. The described procedure can easily be generalized and combined with various affinity tags at the C-terminus for chromatographic applications.
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Affiliation(s)
- Heba A H Abd Elhameed
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Enikő Hermann
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary.
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23
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Nguyen DD, Jones NC, Hoffmann SV, Spanget-Larsen J. Electronic states of dibenzo-p-dioxin. A synchrotron radiation linear dichroism investigation. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Izumi Y, Matsuo K. Sample Volume Reduction Using the Schwarzschild Objective for a Circular Dichroism Spectrophotometer and an Application to the Structural Analysis of Lysine-36 Trimethylated Histone H3 Protein. Molecules 2018; 23:E2865. [PMID: 30400257 PMCID: PMC6278440 DOI: 10.3390/molecules23112865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022] Open
Abstract
With the increasing interest in scarce proteins, reducing the sample volume for circular dichroism (CD) spectroscopy has become desirable. Demagnification of the incident beam size is required to reduce the sample volume for CD spectroscopy detecting transmitted light passed through the sample. In this study, the beam size was demagnified using a focal mirror, and small-capacity sample cells were developed in an attempt to reduce the sample volume. The original beam size was 6 × 6 mm²; we successfully converged it to a size of 25 × 25 μm² using the Schwarzschild objective (SO). The new sample cell and SO allowed the required sample volume to be reduced to 1/10 (15 → 1.5 μL), when using a 15 μm path length cell. By adopting a smaller sample cell, further sample reduction could be achieved. By using the SO system, the secondary structural contents of the lysine-36 trimethylated histone H3 protein were analyzed. The trimethylation induced the increment of helix structures and decrement of unordered structures. These structural alterations may play a role in regulating cellular function(s), such as DNA damage repair processes.
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Affiliation(s)
- Yudai Izumi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
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Hussain R, Longo E, Siligardi G. UV-Denaturation Assay to Assess Protein Photostability and Ligand-Binding Interactions Using the High Photon Flux of Diamond B23 Beamline for SRCD. Molecules 2018; 23:molecules23081906. [PMID: 30065161 PMCID: PMC6222506 DOI: 10.3390/molecules23081906] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022] Open
Abstract
Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host–ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD.
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Affiliation(s)
- Rohanah Hussain
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
| | - Edoardo Longo
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
| | - Giuliano Siligardi
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot OX11 0DE, UK.
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Bortolini C, Klausen LH, Hoffmann SV, Jones NC, Saadeh D, Wang Z, Knowles TPJ, Dong M. Rapid Growth of Acetylated Aβ(16-20) into Macroscopic Crystals. ACS NANO 2018; 12:5408-5416. [PMID: 29771495 DOI: 10.1021/acsnano.8b00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aberrant assembly of the amyloid-β (Aβ) is responsible for the development of Alzheimer's disease, but can also be exploited to obtain highly functional biomaterials. The short Aβ fragment, KLVFF (Aβ16-20), is crucial for Aβ assembly and considered to be an Aβ aggregation inhibitor. Here, we show that acetylation of KLVFF turns it into an extremely fast self-assembling molecule, reaching macroscopic ( i.e., mm) size in seconds. We show that KLVFF is metastable and that the self-assembly can be directed toward a crystalline or fibrillar phase simply through chemical modification, via acetylation or amidation of the peptide. Amidated KLVFF can form amyloid fibrils; we observed folding events of such fibrils occurring in as little as 60 ms. The ability of single KLVFF molecules to rapidly assemble as highly ordered macroscopic structures makes it a promising candidate for applications as a rapid-forming templating material.
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Affiliation(s)
- Christian Bortolini
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Lasse Hyldgaard Klausen
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | | | - Nykola C Jones
- ISA, Department of Physics and Astronomy , Aarhus University , Aarhus 8000 , Denmark
| | - Daniela Saadeh
- Centre for Astronomy & Particle Theory , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Zegao Wang
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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Madsen MM, Jones NC, Nielsen SB, Hoffmann SV. On the wavelength dependence of UV induced thymine photolesions: a synchrotron radiation circular dichroism study. Phys Chem Chem Phys 2018; 18:30436-30443. [PMID: 27781221 DOI: 10.1039/c6cp05980e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Solar mutagenesis via the formation of thymine dimer photoproducts is a primary cause of skin cancer. The aim of this study is to provide a direct method for following the development of photolesions in thymine single strands and to determine how the formation of these photoproducts depends on the excitation wavelength in the ultraviolet (UV) between 210 nm and 325 nm. Experiments were performed both with a 20 Hz pulsed, intense, tunable laser as well as UV lamps (at 254 nm and 302 nm), but we find that only the dose matters at these wavelengths for the yield of photoproducts. Hence in both cases the lesion process is due to one-photon absorption. The formation and yields of the photoproducts as the irradiation dose is increased is followed through measurement of synchrotron radiation circular dichroism (SRCD) spectra. A principal component analysis (PCA) of the SRCD data yields CD signatures for each of the resulting photoproducts and reveals a strong irradiation wavelength dependence upon which products are formed; cyclobutane pyrimidine dimers (CPDs) are formed primarily at higher irradiation wavelengths (from 250 to 300 nm); the 6,4 pyrimidine-pyrimidone photoadduct (64PP) is formed in the range 210 to 285 nm, with a higher rate of formation in the lower part of that range, while in the very lowest irradiation wavelength range (210 to 240 nm) we find thymidine monophosphate (dTMP), which indicates cleavage of the DNA backbone. Our work demonstrates the strength of SRCD spectroscopy compared to ordinary absorption spectroscopy, as the latter is not sufficient to obtain fingerprints of the thymine photoproducts.
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Affiliation(s)
- Marlene Møller Madsen
- Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark. and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Nykola C Jones
- Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark.
| | - Steen Brøndsted Nielsen
- Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark.
| | - Søren Vrønning Hoffmann
- Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark.
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Nguyen DD, Jones NC, Hoffmann SV, Spanget-Larsen J. Vacuum UV Polarization Spectroscopy of p-Terphenyl. J Phys Chem A 2018; 122:184-191. [PMID: 29207234 DOI: 10.1021/acs.jpca.7b10442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
p-Terphenyl is used as a component in a variety of optical devices. In this investigation, the electronic transitions of p-terphenyl are investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 30000-58000 cm-1 (330-170 nm) on molecular samples aligned in stretched polyethylene, thereby extending the region investigated by polarization spectroscopy into the vacuum UV. The resulting partial absorbance curves reveal that the vacuum UV band system with a maximum at 55000 cm-1 (180 nm) is predominantly short axis-polarized. This result is of interest in the optical applications of p-terphenyl, for example as a wavelength shifter. The observed polarization spectra are compared with the results of quantum chemical model calculations. Convoluted versions of the transitions predicted with the semiempirical ZINDO method and with the long-range-corrected time-dependent density functional theory (TD-DFT) procedures TD-CAM-B3LYP, TD-LC-ωPBE, and TD-ωB97XD are in similar qualitative agreement with the observed partial absorbance curves throughout the investigated spectral regions, while TD-B3LYP fails to predict qualitatively the spectrum of p-terphenyl in the region above 40000 cm-1 (250 nm).
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Affiliation(s)
- Duy Duc Nguyen
- Department of Science and Environment, Roskilde University , Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University , Ny Munkegade 120, Bldg. 1520, DK-8000 Aarhus C, Denmark
| | - Søren V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University , Ny Munkegade 120, Bldg. 1520, DK-8000 Aarhus C, Denmark
| | - Jens Spanget-Larsen
- Department of Science and Environment, Roskilde University , Universitetsvej 1, DK-4000 Roskilde, Denmark
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29
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Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease. Chembiochem 2017; 19:66-75. [DOI: 10.1002/cbic.201700420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Indexed: 01/20/2023]
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The pH-dependent assembly of Chaplin E from Streptomyces coelicolor. J Struct Biol 2017; 198:82-91. [PMID: 28400129 DOI: 10.1016/j.jsb.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/06/2017] [Accepted: 04/07/2017] [Indexed: 01/01/2023]
Abstract
Chaplin E, is one of five self-assembling peptides secreted by Streptomyces coelicolor that assist aerial growth by lowering the surface tension of water. Although the surface activity of a mixture of chaplin peptides has observed to depend on pH, it is unclear how the solvent environment (i.e. pH) influences the structure, assembly and subsequent functionality of these individual peptides. In this study, the conformation and fibril forming propensity of the Chaplin E peptide was assessed as a function of pH using a combination of experimental measurements and molecular dynamics simulations. At an acidic pH of 3.0, Chaplin E retained a random coil structure, whereas at the isoelectric point of 6.7 or a basic pH of 10.0, Chaplin E rapidly formed amyloid fibrils rich in β-sheet structure with high efficiency (>93%). Molecular dynamics simulations indicate the persistence of greater α-helical content at the N-terminus at high pH; this is likely partly due to the lack of electrostatic repulsion between residues His6 and Lys10. Since fibril formation was observed at high but not at low pH, we propose that the presence of an N-terminal α-helix in the monomeric form of Chaplin E is required for aggregation and conversion to β-amyloid fibrils. The pH sensitivity of Chaplin E peptide structure provides a route to control peptide assembly and may be important for the physiological function of this peptide, as a surface active agent in the transition from vegetative to aerial growth and could assist Streptomyces coelicolor in response to environmental fluctuations in pH.
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31
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Meinert C, Jones NC, Hoffmann SV, Meierhenrich UJ. Anisotropy spectroscopy of chiral alcohols, amines, and monocarboxylic acids: Implications for the analyses of extraterrestrial samples. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Németh E, Balogh RK, Borsos K, Czene A, Thulstrup PW, Gyurcsik B. Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study. Protein Sci 2016; 25:1977-1988. [PMID: 27508941 DOI: 10.1002/pro.3010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/08/2016] [Indexed: 12/21/2022]
Abstract
X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary.,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Katalin Borsos
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Anikó Czene
- MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary. .,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary.
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33
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Liu L, Li Q, Zhang S, Wang X, Hoffmann SV, Li J, Liu Z, Besenbacher F, Dong M. Identification of a Novel Parallel β-Strand Conformation within Molecular Monolayer of Amyloid Peptide. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2016; 3:1500369. [PMID: 27818898 PMCID: PMC5071675 DOI: 10.1002/advs.201500369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Indexed: 05/27/2023]
Abstract
The differentiation of protein properties and biological functions arises from the variation in the primary and secondary structure. Specifically, in abnormal assemblies of protein, such as amyloid peptide, the secondary structure is closely correlated with the stable ensemble and the cytotoxicity. In this work, the early Aβ33-42 aggregates forming the molecular monolayer at hydrophobic interface are investigated. The molecular monolayer of amyloid peptide Aβ33-42 consisting of novel parallel β-strand-like structure is further revealed by means of a quantitative nanomechanical spectroscopy technique with force controlled in pico-Newton range, combining with molecular dynamic simulation. The identified parallel β-strand-like structure of molecular monolayer is distinct from the antiparallel β-strand structure of Aβ33-42 amyloid fibril. This finding enriches the molecular structures of amyloid peptide aggregation, which could be closely related to the pathogenesis of amyloid disease.
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Affiliation(s)
- Lei Liu
- Institute for Advanced Materials Jiangsu University Zhenjiang 212013 P. R. China; Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus CDK-8000 Denmark
| | - Qiang Li
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C DK-8000 Denmark
| | - Shuai Zhang
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C DK-8000 Denmark
| | - Xiaofeng Wang
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 P. R. China
| | | | - Jingyuan Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zheng Liu
- Center for Programmable Materials School of Materials Science and Engineering Nanyang Technological University Singapore Singapore 639798 Singapore
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C DK-8000 Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C DK-8000 Denmark
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Pages BJ, Sakoff J, Gilbert J, Rodger A, Chmel NP, Jones NC, Kelly SM, Ang DL, Aldrich-Wright JR. Multifaceted Studies of the DNA Interactions and In Vitro Cytotoxicity of Anticancer Polyaromatic Platinum(II) Complexes. Chemistry 2016; 22:8943-54. [DOI: 10.1002/chem.201601221] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Benjamin J. Pages
- Nanoscale Organisation and Dynamics Group; Western Sydney University; Campbelltown NSW 2560 Australia
| | | | | | - Alison Rodger
- Department of Chemistry; University of Warwick; Coventry West Midlands CV47AL UK
| | - Nikola P. Chmel
- Department of Chemistry; University of Warwick; Coventry West Midlands CV47AL UK
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy; Aarhus University; Aarhus 8000 Denmark
| | - Sharon M. Kelly
- Institute of Molecular, Cell and Systems Biology; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ UK
| | - Dale L. Ang
- Nanoscale Organisation and Dynamics Group; Western Sydney University; Campbelltown NSW 2560 Australia
| | - Janice R. Aldrich-Wright
- Nanoscale Organisation and Dynamics Group; Western Sydney University; Campbelltown NSW 2560 Australia
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35
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Nedzhib A, Kessler J, Bouř P, Gyurcsik B, Pantcheva I. Circular Dichroism is Sensitive to Monovalent Cation Binding in Monensin Complexes. Chirality 2016; 28:420-8. [PMID: 27062535 DOI: 10.1002/chir.22597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/08/2022]
Abstract
Monensin is a natural antibiotic that exhibits high affinity to certain metal ions. In order to explore its potential in coordination chemistry, circular dichroism (CD) spectra of monensic acid A (MonH) and its derivatives containing monovalent cations (Li(+) , Na(+) , K(+) , Rb(+) , Ag(+) , and Et4 N(+) ) in methanolic solutions were measured and compared to computational models. Whereas the conventional CD spectroscopy allowed recording of the transitions down to 192 nm, synchrotron radiation circular dichroism (SRCD) revealed other bands in the 178-192 nm wavelength range. CD signs and intensities significantly varied in the studied compounds, in spite of their similar crystal structure. Computational modeling based on the Density Functional Theory (DFT) and continuum solvent model suggests that the solid state monensin structure is largely conserved in the solutions as well. Time-dependent Density Functional Theory (TDDFT) simulations did not allow band-to-band comparison with experimental spectra due to their limited precision, but indicated that the spectral changes were caused by a combination of minor conformational changes upon the monovalent cation binding and a direct involvement of the metal electrons in monensin electronic transitions. Both the experiment and simulations thus show that the CD spectra of monensin complexes are very sensitive to the captured ions and can be used for their discrimination. Chirality 28:420-428, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ahmed Nedzhib
- Department of Analytical Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski,", Sofia, Bulgaria
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, Hungary
| | - Ivayla Pantcheva
- Department of Analytical Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski,", Sofia, Bulgaria
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36
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Bortolini C, Dong M. Cystine oligomers successfully attached to peptide cysteine-rich fibrils. Front Chem Sci Eng 2016. [DOI: 10.1007/s11705-016-1554-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Bortolini C, Jones NC, Hoffmann SV, Besenbacher F, Dong M. The influence of the localised charge of C- and N-termini on peptide self-assembly. SOFT MATTER 2016; 12:373-377. [PMID: 26472087 DOI: 10.1039/c5sm01669j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The charge of a peptide influences final assembled structures. It is important to consider not only global charge, but also local, such as that found on the terminal residues. This work investigates the change of peptide self-assembly through the selection of different amino acid sequences and by varying the local charge of the residues on the C- and N-termini.
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Affiliation(s)
- C Bortolini
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds 14, Building 1590, Aarhus C, Denmark.
| | - N C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
| | - S V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
| | - F Besenbacher
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds 14, Building 1590, Aarhus C, Denmark.
| | - M Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds 14, Building 1590, Aarhus C, Denmark.
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38
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Preorganization of the catalytic Zn2+-binding site in the HNH nuclease motif—A solution study. J Inorg Biochem 2015; 151:143-9. [DOI: 10.1016/j.jinorgbio.2015.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
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39
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Szunyogh D, Gyurcsik B, Larsen FH, Stachura M, Thulstrup PW, Hemmingsen L, Jancsó A. Zn(II) and Hg(II) binding to a designed peptide that accommodates different coordination geometries. Dalton Trans 2015; 44:12576-88. [PMID: 26040991 DOI: 10.1039/c5dt00945f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Designed metal ion binding peptides offer a variety of applications in both basic science as model systems of more complex metalloproteins, and in biotechnology, e.g. in bioremediation of toxic metal ions, biomining or as artificial enzymes. In this work a peptide (HS: Ac-SCHGDQGSDCSI-NH2) has been specifically designed for binding of both Zn(II) and Hg(II), i.e. metal ions with different preferences in terms of coordination number, coordination geometry, and to some extent ligand composition. It is demonstrated that HS accommodates both metal ions, and the first coordination sphere, metal ion exchange between peptides, and speciation are characterized as a function of pH using UV-absorption-, synchrotron radiation CD-, (1)H-NMR-, and PAC-spectroscopy as well as potentiometry. Hg(II) binds to the peptide with very high affinity in a {HgS2} coordination geometry, bringing together the two cysteinates close to each end of the peptide in a loop structure. Despite the high affinity, Hg(II) is kinetically labile, exchanging between peptides on the subsecond timescale, as indicated by line broadening in (1)H-NMR. The Zn(II)-HS system displays more complex speciation, involving monomeric species with coordinating cysteinates, histidine, and a solvent water molecule, as well as HS-Zn(II)-HS complexes. In summary, the HS peptide displays conformational flexibility, contains many typical metal ion binding groups, and is able to accommodate metal ions with different structural and ligand preferences with high affinity. As such, the HS peptide may be a scaffold offering binding of a variety of metal ions, and potentially serve for metal ion sequestration in biotechnological applications.
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Affiliation(s)
- Dániel Szunyogh
- MTA-SZTE Bioinorganic Chemistry Research Group, Dóm tér 7, Szeged, H-6720, Hungary
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Bortolini C, Jones NC, Hoffmann SV, Wang C, Besenbacher F, Dong M. Mechanical properties of amyloid-like fibrils defined by secondary structures. NANOSCALE 2015; 7:7745-7752. [PMID: 25839069 DOI: 10.1039/c4nr05109b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils.
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Affiliation(s)
- C Bortolini
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds 14, Building 1590, Aarhus C., Denmark.
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Bürck J, Roth S, Windisch D, Wadhwani P, Moss D, Ulrich AS. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:844-52. [PMID: 25931105 PMCID: PMC4416691 DOI: 10.1107/s1600577515004476] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts.
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Affiliation(s)
- Jochen Bürck
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Siegmar Roth
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Dirk Windisch
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - David Moss
- ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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Kläning E, Christensen B, Bajic G, Hoffmann SV, Jones NC, Callesen MM, Andersen GR, Sørensen ES, Vorup-Jensen T. Multiple low-affinity interactions support binding of human osteopontin to integrin αXβ2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:930-8. [PMID: 25839998 DOI: 10.1016/j.bbapap.2015.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/18/2015] [Accepted: 03/22/2015] [Indexed: 01/11/2023]
Abstract
Integrin α(X)β(2) (also known as complement receptor 4, p150,95, or CD11c/CD18) is expressed in the cell membrane of myeloid leukocytes. α(X)β(2) has been reported to bind a large number of structurally unrelated ligands, often with a shared molecular character in the presence of polyanionic stretches in poorly folded proteins or glucosaminoglycans. Nevertheless, it is unclear what chemical sources of polyanionicity enable the binding by α(X)β(2). Osteopontin (OPN) is an intrinsically disordered protein, which facilitates phagocytosis via the integrin α(X)β(2). Unlike for other integrins, neither the RGD nor the SVVYGLR motifs account for this binding, and the molecular basis of OPN binding by α(X)β(2) remains uncharacterized. Here, we show that the monovalent interactions between the ligand-binding domain of α(X)β(2) and OPN, its fragments, or caseins are weak, with dissociation constants higher than 10(-5)M but with high apparent stoichiometries. From comparison with cell adhesion studies, the discrimination between α(X)β(2) ligands and non-ligands appears to rely on these apparent stoichiometries in a way, which involves glutamate rather than aspartate side chains. Surprisingly, the extensive, negatively charged phosphorylation of OPN is not contributing to α(X)β(2) binding. Furthermore, synchrotron radiation circular spectroscopy excludes that the phosphorylation affects the general folding of OPN. Taken together, our quantitative analyses reveal a mode of ligand recognition by integrin α(X)β(2), which seem to differ in principles considerably from other OPN receptors.
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Affiliation(s)
- Eva Kläning
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark; Dept. of Biomedicine, Denmark
| | - Brian Christensen
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark
| | - Goran Bajic
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark
| | - Søren V Hoffmann
- Institute for Storage Ring Facilities Aarhus (ISA), Dept. of Physics and Astronomy & Center for Storage Ring Facilities Aarhus, Denmark
| | - Nykola C Jones
- Institute for Storage Ring Facilities Aarhus (ISA), Dept. of Physics and Astronomy & Center for Storage Ring Facilities Aarhus, Denmark
| | - Morten M Callesen
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark
| | - Gregers R Andersen
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark
| | - Esben S Sørensen
- Dept. of Molecular Biology and Genetics Aarhus University, Aarhus, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus Denmark
| | - Thomas Vorup-Jensen
- Dept. of Biomedicine, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus Denmark; MEMBRANES Research Center, Aarhus University, Aarhus, Denmark.
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Gorgel M, Ulstrup JJ, Bøggild A, Jones NC, Hoffmann SV, Nissen P, Boesen T. High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis. BMC STRUCTURAL BIOLOGY 2015; 15:4. [PMID: 25886849 PMCID: PMC4376143 DOI: 10.1186/s12900-015-0031-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/02/2015] [Indexed: 11/10/2022]
Abstract
Background Type IV pili are widely expressed among Gram-negative bacteria, where they are involved in biofilm formation, serve in the transfer of DNA, motility and in the bacterial attachment to various surfaces. Type IV pili in Shewanella oneidensis are also supposed to play an important role in extracellular electron transfer by the attachment to sediments containing electron acceptors and potentially forming conductive nanowires. Results The potential nanowire type IV pilin PilBac1 from S. oneidensis was characterized by a combination of complementary structural methods and the atomic structure was determined at a resolution of 1.67 Å by X-ray crystallography. PilBac1 consists of one long N-terminal α-helix packed against four antiparallel β-strands, thus revealing the core fold of type IV pilins. In the crystal, PilBac1 forms a parallel dimer with a sodium ion bound to one of the monomers. Interestingly, our PilBac1 crystal structure reveals two unusual features compared to other type IVa pilins: an unusual position of the disulfide bridge and a straight α-helical section, which usually exhibits a pronounced kink. This straight helix leads to a distinct packing in a filament model of PilBac1 based on an EM model of a Neisseria pilus. Conclusions In this study we have described the first structure of a pilin from Shewanella oneidensis. The structure possesses features of the common type IV pilin core, but also exhibits significant variations in the α-helical part and the D-region. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0031-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manuela Gorgel
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark.
| | - Jakob Jensen Ulstrup
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark.
| | - Andreas Bøggild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark.
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, building 1525, Aarhus C, 8000, Denmark.
| | - Søren V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, building 1525, Aarhus C, 8000, Denmark.
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark.
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark.
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Substrate binding activates the designed triple mutant of the colicin E7 metallonuclease. J Biol Inorg Chem 2014; 19:1295-303. [DOI: 10.1007/s00775-014-1186-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
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Németh E, Körtvélyesi T, Thulstrup PW, Christensen HEM, Kožíšek M, Nagata K, Czene A, Gyurcsik B. Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations. Protein Sci 2014; 23:1113-22. [PMID: 24895333 DOI: 10.1002/pro.2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 11/11/2022]
Abstract
The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C-terminal HNH motif. Interestingly, the deletion of four N-terminal residues (446-449 NColE7 = KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuclease activity, but a detailed analysis of the role of the highly positive and flexible N-terminus is still missing. Here, we present the study of four mutants, with a decreased activity in the following order: NColE7 >> KGNK > KGNG ∼ GGNK > GGNG. At the same time, the folding, the metal-ion, and the DNA-binding affinity were unaffected by the mutations as revealed by linear and circular dichroism spectroscopy, isothermal calorimetric titrations, and gel mobility shift experiments. Semiempirical quantum chemical calculations and molecular dynamics simulations revealed that K446, K449, and/or the N-terminal amino group are able to approach the active centre in the absence of the other positively charged residues. The results suggested a complex role of the N-terminus in the catalytic process that could be exploited in the design of a controlled nuclease.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, 6720, Szeged, Hungary; Department of Physical Chemistry and Material Sciences, University of Szeged, 6720, Szeged, Hungary
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Bredehöft JH, Jones NC, Meinert C, Evans AC, Hoffmann SV, Meierhenrich UJ. Understanding Photochirogenesis: Solvent Effects on Circular Dichroism and Anisotropy Spectroscopy. Chirality 2014; 26:373-8. [DOI: 10.1002/chir.22329] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/15/2014] [Indexed: 11/11/2022]
Affiliation(s)
| | - Nykola C. Jones
- ISA, Dept. of Physics and Astronomy; Aarhus University; Aarhus Denmark
| | - Cornelia Meinert
- Institut de Chimie de Nice ICN; Université de Nice-Sophia Antipolis; Nice France
| | - Amanda C. Evans
- Institut de Chimie de Nice ICN; Université de Nice-Sophia Antipolis; Nice France
- University of Cambridge; Murray Edwards College; Cambridge United Kingdom
| | - Søren V. Hoffmann
- ISA, Dept. of Physics and Astronomy; Aarhus University; Aarhus Denmark
| | - Uwe J. Meierhenrich
- Institut de Chimie de Nice ICN; Université de Nice-Sophia Antipolis; Nice France
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Nielsen LM, Hoffmann SV, Nielsen SB. Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated. Photochem Photobiol Sci 2014; 12:1273-85. [PMID: 23545881 DOI: 10.1039/c3pp25438k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.
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Cook AM, Mattioda AL, Ricco AJ, Quinn RC, Elsaesser A, Ehrenfreund P, Ricca A, Jones NC, Hoffmann SV. The Organism/Organic Exposure to Orbital Stresses (O/OREOS) satellite: radiation exposure in low-earth orbit and supporting laboratory studies of iron tetraphenylporphyrin chloride. ASTROBIOLOGY 2014; 14:87-101. [PMID: 24512475 DOI: 10.1089/ast.2013.0998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report results from the exposure of the metalloporphyrin iron tetraphenylporphyrin chloride (FeTPPCl) to the outer space environment, measured in situ aboard the Organism/Organic Exposure to Orbital Stresses nanosatellite. FeTPPCl was exposed for a period of 17 months (3700 h of direct solar exposure), which included broad-spectrum solar radiation (∼122 nm to the near infrared). Motivated by the potential role of metalloporphyrins as molecular biomarkers, the exposure of thin-film samples of FeTPPCl to the space environment in low-Earth orbit was monitored in situ via ultraviolet/visible spectroscopy and reported telemetrically. The space data were complemented by laboratory exposure experiments that used a high-fidelity solar simulator covering the spectral range of the spaceflight measurements. We found that thin-film samples of FeTPPCl that were in contact with a humid headspace gas (0.8-2.3% relative humidity) were particularly susceptible to destruction upon irradiation, degrading up to 10 times faster than identical thin films in contact with dry headspace gases; this degradation may also be related to the presence of oxides of nitrogen in those cells. In the companion terrestrial experiments, simulated solar exposure of FeTPPCl films in contact with either Ar or CO2:O2:Ar (10:0.01:1000) headspace gas resulted in growth of a band in the films' infrared spectra at 1961 cm(-1). We concluded that the most likely carriers of this band are allene (C3H4) and chloropropadiene (C3H3Cl), putative molecular fragments of the destruction of the porphyrin ring. The thin films studied in space and in solar simulator-based experiments show qualitatively similar spectral evolution as a function of contacting gaseous species but display significant differences in the time dependence of those changes. The relevance of our findings to planetary science, biomarker research, and the photostability of organic materials in astrobiologically relevant environments is discussed.
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Affiliation(s)
- Amanda M Cook
- 1 NASA Ames Research Center , Moffett Field, California, USA
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Day L, Zhai J, Xu M, Jones NC, Hoffmann SV, Wooster TJ. Conformational changes of globular proteins adsorbed at oil-in-water emulsion interfaces examined by Synchrotron Radiation Circular Dichroism. Food Hydrocoll 2014. [DOI: 10.1016/j.foodhyd.2012.12.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Wyer JA, Kristensen MB, Jones NC, Hoffmann SV, Nielsen SB. Kinetics of DNA duplex formation: A-tracts versus AT-tracts. Phys Chem Chem Phys 2014; 16:18827-39. [DOI: 10.1039/c4cp02252a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A-tracts (AAAA…:TTTT…) form much faster than AT-tracks (ATAT…:TATA…).
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Affiliation(s)
- Jean Ann Wyer
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C, Denmark
| | | | - Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C, Denmark
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