601
|
Le Brun E, Arluison V, Wien F. Application of Synchrotron Radiation Circular Dichroism for RNA Structural Analysis. Methods Mol Biol 2020; 2113:135-148. [PMID: 32006313 DOI: 10.1007/978-1-0716-0278-2_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular dichroism (CD) spectroscopy is a fast and simple technique providing important information about the conformation of nucleic acids, proteins, sugars, lipids, and their interactions between each other. This electronic absorption spectroscopy method is extremely sensitive to any change in molecular structure containing asymmetric molecules. While numerous reviews describe how to analyze deoxyribonucleic acid (DNA) structures using CD, analyses of ribonucleic acids (RNAs) are scarce. Nevertheless, RNAs are important molecules involved in a multitude of roles in the cell. In this chapter, we present applications of synchrotron radiation circular dichroism (SRCD) extending the spectral range down to 170 nm, improving structural analysis of RNA, including the analysis of helical parameters and alternative structures found in RNA. The effects of temperature to measure thermodynamic parameters and analyze ribonucleoprotein complexes will also be presented.
Collapse
Affiliation(s)
- Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France
- Université de Paris, Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France.
| |
Collapse
|
602
|
Colagiorgi A, Festa R, Di Ciccio PA, Gogliettino M, Balestrieri M, Palmieri G, Anastasio A, Ianieri A. Rapid biofilm eradication of the antimicrobial peptide 1018-K6 against Staphylococcus aureus: A new potential tool to fight bacterial biofilms. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106815] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
603
|
Yamamoto H, Fukui N, Adachi M, Saiki E, Yamasaki A, Matsumura R, Kuroyanagi D, Hongo K, Mizobata T, Kawata Y. Human Molecular Chaperone Hsp60 and Its Apical Domain Suppress Amyloid Fibril Formation of α-Synuclein. Int J Mol Sci 2019; 21:ijms21010047. [PMID: 31861692 PMCID: PMC6982183 DOI: 10.3390/ijms21010047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/14/2023] Open
Abstract
Heat shock proteins play roles in assisting other proteins to fold correctly and in preventing the aggregation and accumulation of proteins in misfolded conformations. However, the process of aging significantly degrades this ability to maintain protein homeostasis. Consequently, proteins with incorrect conformations are prone to aggregate and accumulate in cells, and this aberrant aggregation of misfolded proteins may trigger various neurodegenerative diseases, such as Parkinson's disease. Here, we investigated the possibilities of suppressing α-synuclein aggregation by using a mutant form of human chaperonin Hsp60, and a derivative of the isolated apical domain of Hsp60 (Hsp60 AD(Cys)). In vitro measurements were used to detect the effects of chaperonin on amyloid fibril formation, and interactions between Hsp60 proteins and α-synuclein were probed by quartz crystal microbalance analysis. The ability of Hsp60 AD(Cys) to suppress α-synuclein intracellular aggregation and cytotoxicity was also demonstrated. We show that Hsp60 mutant and Hsp60 AD(Cys) both effectively suppress α-synuclein amyloid fibril formation, and also demonstrate for the first time the ability of Hsp60 AD(Cys) to function as a mini-chaperone inside cells. These results highlight the possibility of using Hsp60 AD as a method of prevention and treatment of neurodegenerative diseases.
Collapse
Affiliation(s)
- Hanae Yamamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
| | - Naoya Fukui
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
| | - Mayuka Adachi
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
| | - Eiichi Saiki
- Department of Chemistry and Biotechnology, Faculty of Engineering, Tottori University, Koyama-Minami, Tottori 680-8552, Japan;
| | - Anna Yamasaki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
| | - Rio Matsumura
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
| | - Daichi Kuroyanagi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
- Department of Chemistry and Biotechnology, Faculty of Engineering, Tottori University, Koyama-Minami, Tottori 680-8552, Japan;
- Center for Research on Green Sustainable Chemistry, Koyama-Minami, Tottori University, Tottori 680-8552, Japan
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
- Department of Chemistry and Biotechnology, Faculty of Engineering, Tottori University, Koyama-Minami, Tottori 680-8552, Japan;
- Center for Research on Green Sustainable Chemistry, Koyama-Minami, Tottori University, Tottori 680-8552, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (H.Y.); (N.F.); (D.K.); (K.H.)
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan; (M.A.); (A.Y.); (R.M.)
- Department of Chemistry and Biotechnology, Faculty of Engineering, Tottori University, Koyama-Minami, Tottori 680-8552, Japan;
- Center for Research on Green Sustainable Chemistry, Koyama-Minami, Tottori University, Tottori 680-8552, Japan
- Correspondence: ; Tel.: +81-857-31-5787
| |
Collapse
|
604
|
Putra RP, Ikumura Y, Horino H, Hori A, Rzeznicka II. Adsorption and Conformation of Bovine Serum Albumin with Blue-Emitting Gold Nanoclusters at the Air/Water and Lipid/Water Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16576-16582. [PMID: 31763843 DOI: 10.1021/acs.langmuir.9b02831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein-encapsulated nanoclusters (NCs) are emerging as a versatile platform for in-vivo imaging and other biomedical applications due to their ultrasmall size and excitation in the near-infrared region. Encapsulation may however affect protein structure, size, charge, and its interaction with lipid membranes. In this study, bulk characterization methods along with surface-sensitive vibrational sum-frequency generation (VSFG) spectroscopy were employed to study the secondary structure of bovine serum albumin (BSA) with blue-emitting Au8NCs at the air/water and 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) lipid/water interfaces. With this approach, the difference in the adsorption behavior between native BSA and BSA with an increasing number of blue-emitting NCs was investigated under different pH conditions. At pH 7, at which both BSA and the lipid are negatively charged, protein molecules are found to associate with the DPPG monolayer via hydrophobic interactions with no preferential orientation across the lipid monolayer. At pH 3, adsorption of BSA at the DPPG monolayer occurs mainly due to electrostatic interactions between the negatively charged lipid headgroups and the positively charged protein, resulting in a uniform orientation of the protein across the lipid monolayer. Complimentary bulk studies by circular dichroism and particle size measurements show that the encapsulation of Au8NCs is associated with the loss of BSA helicity, which makes BSA-encapsulated Au8NCs prone to oligomerization, especially at a high content of Au8NCs at one BSA protein. The results indicate that the hydrodynamic diameter of BSA with Au8NCs strongly depends on the molar fraction of gold, the pH, and the storage time. A prolonged storage of Au8NCs@BSA at pH 7 increases the rate of protein oligomerization.
Collapse
Affiliation(s)
- Ridwan P Putra
- Graduate School of Engineering and Science , Shibaura Institute of Technology , Fukasaku 307 , 337-8570 Saitama , Japan
| | - Yoshinori Ikumura
- Graduate School of Engineering and Science , Shibaura Institute of Technology , Fukasaku 307 , 337-8570 Saitama , Japan
| | - Hideyuki Horino
- Department of Chemistry for Materials, Graduate School of Engineering , Mie University , 1577 Kurimamachiya-cho , 514-8507 Tsu , Mie , Japan
| | - Akiko Hori
- Graduate School of Engineering and Science , Shibaura Institute of Technology , Fukasaku 307 , 337-8570 Saitama , Japan
| | - Izabela I Rzeznicka
- Graduate School of Engineering and Science , Shibaura Institute of Technology , Fukasaku 307 , 337-8570 Saitama , Japan
| |
Collapse
|
605
|
Vurgun N, Nitz M. Validation of l-Tellurienylalanine as a Phenylalanine Isostere. Chembiochem 2019; 21:1136-1139. [PMID: 31742805 DOI: 10.1002/cbic.201900635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Indexed: 01/21/2023]
Abstract
Mass cytometry (MC) and imaging mass cytometry (IMCTM ) have emerged as important tools for the study of biological heterogeneity. We recently demonstrated the use of l-2-tellurienylalanine (TePhe), a mimic of phenylalanine (Phe), as an MC- and IMC-compatible protein synthesis reporter. In this work, the biochemical similarity of TePhe and its cognate analogue, Phe, are examined in the context of the RNase S complex. Isothermal titration calorimetry studies show that incorporation of TePhe preserves the interaction of S-peptide with S-protein, and the dissociation constants for the interaction of the Phe and TePhe peptides are within a factor of two. The resulting RNase S complex is catalytically active without significant alterations in the enzyme's kinetic parameters. Furthermore, circular dichroism spectroscopy does not reveal any changes to the secondary structure of TePhe-substituted RNase S. These findings provide strong evidence that TePhe functions as a Phe isostere in the context of a folded protein. It is anticipated that incorporation of TePhe into peptides or peptidomimetic scaffolds will enable facile generation of MC and IMCTM probes.
Collapse
Affiliation(s)
- Nesrin Vurgun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| |
Collapse
|
606
|
Laurent CV, Sun P, Scheiblbrandner S, Csarman F, Cannazza P, Frommhagen M, van Berkel WJ, Oostenbrink C, Kabel MA, Ludwig R. Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity. Int J Mol Sci 2019; 20:E6219. [PMID: 31835532 PMCID: PMC6940765 DOI: 10.3390/ijms20246219] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 12/07/2019] [Indexed: 12/29/2022] Open
Abstract
In past years, new lytic polysaccharide monooxygenases (LPMOs) have been discovered as distinct in their substrate specificity. Their unconventional, surface-exposed catalytic sites determine their enzymatic activities, while binding sites govern substrate recognition and regioselectivity. An additional factor influencing activity is the presence or absence of a family 1 carbohydrate binding module (CBM1) connected via a linker to the C-terminus of the LPMO. This study investigates the changes in activity induced by shortening the second active site segment (Seg2) or removing the CBM1 from Neurospora crassa LPMO9C. NcLPMO9C and generated variants have been tested on regenerated amorphous cellulose (RAC), carboxymethyl cellulose (CMC) and xyloglucan (XG) using activity assays, conversion experiments and surface plasmon resonance spectroscopy. The absence of CBM1 reduced the binding affinity and activity of NcLPMO9C, but did not affect its regioselectivity. The linker was found important for the thermal stability of NcLPMO9C and the CBM1 is necessary for efficient binding to RAC. Wild-type NcLPMO9C exhibited the highest activity and strongest substrate binding. Shortening of Seg2 greatly reduced the activity on RAC and CMC and completely abolished the activity on XG. This demonstrates that Seg2 is indispensable for substrate recognition and the formation of productive enzyme-substrate complexes.
Collapse
Affiliation(s)
- Christophe V.F.P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Florian Csarman
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Pietro Cannazza
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| |
Collapse
|
607
|
Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nat Commun 2019; 10:5612. [PMID: 31819058 PMCID: PMC6901522 DOI: 10.1038/s41467-019-13577-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human myeloid-derived growth factor (hMYDGF) is a 142-residue protein with a C-terminal endoplasmic reticulum (ER) retention sequence (ERS). Extracellular MYDGF mediates cardiac repair in mice after anoxic injury. Although homologs of hMYDGF are found in eukaryotes as distant as protozoans, its structure and function are unknown. Here we present the NMR solution structure of hMYDGF, which consists of a short α-helix and ten β-strands distributed in three β-sheets. Conserved residues map to the unstructured ERS, loops on the face opposite the ERS, and the surface of a cavity underneath the conserved loops. The only protein or portion of a protein known to have a similar fold is the base domain of VNN1. We suggest, in analogy to the tethering of the VNN1 nitrilase domain to the plasma membrane via its base domain, that MYDGF complexed to the KDEL receptor binds cargo via its conserved residues for transport to the ER.
Collapse
Affiliation(s)
- Valeriu Bortnov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Woonghee Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ziqing Lin
- Departments of Cell and Regenerative Biology and Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Douglas S Annis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Omar N Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ying Ge
- Departments of Cell and Regenerative Biology and Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
608
|
Immunogenic Properties of Recombinant Enzymes from Bothrops Ammodytoides Towards the Generation of Neutralizing Antibodies against Its Own Venom. Toxins (Basel) 2019; 11:toxins11120702. [PMID: 31810356 PMCID: PMC6949999 DOI: 10.3390/toxins11120702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 11/23/2022] Open
Abstract
Bothropic venoms contain enzymes such as metalloproteases, serine-proteases, and phospholipases, which acting by themselves, or in synergism, are the cause of the envenomation symptoms and death. Here, two mRNA transcripts, one that codes for a metalloprotease and another for a serine-protease, were isolated from a Bothrops ammodytoides venom gland. The metalloprotease and serine-protease transcripts were cloned on a pCR®2.1-TOPO vector and consequently expressed in a recombinant way in E. coli (strains Origami and M15, respectively), using pQE30 vectors. The recombinant proteins were named rBamSP_1 and rBamMP_1, and they were formed by an N-terminal fusion protein of 16 amino acid residues, followed by the sequence of the mature proteins. After bacterial expression, each recombinant enzyme was recovered from inclusion bodies and treated with chaotropic agents. The experimental molecular masses for rBamSP_1 and rBamMP_1 agreed with their expected theoretical ones, and their secondary structure spectra obtained by circular dichroism were comparable to that of similar proteins. Additionally, equivalent mixtures of rBamSP_1, rBamMP_1 together with a previous reported recombinant phospholipase, rBamPLA2_1, were used to immunize rabbits to produce serum antibodies, which in turn recognized serine-proteases, metalloproteases and PLA2s from B. ammodytoides and other regional viper venoms. Finally, rabbit antibodies neutralized the 3LD50 of B. ammodytoides venom.
Collapse
|
609
|
Choukate K, Gupta A, Basu B, Virk K, Ganguli M, Chaudhuri B. Higher order assembling of the mycobacterial polar growth factor DivIVA/Wag31. J Struct Biol 2019; 209:107429. [PMID: 31778770 DOI: 10.1016/j.jsb.2019.107429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/04/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022]
Abstract
DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structural organization of polar scaffold formed by polymerization of coiled-coil rich Wag31, which is implicated in the anti-tubercular activities of amino-pyrimidine sulfonamides, remains to be determined. A single-site phosphorylation in Wag31 regulates peptidoglycan biosynthesis in mycobacteria. We report biophysical characterizations of filaments formed by mycobacterial Wag31 using circular dichroism, atomic force microscopy and small angle solution X-ray scattering. Atomic force microscopic images of the wild-type, a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of Wag31 show mostly linear filament formation with occasional curving, kinking and apparent branching. Solution X-ray scattering data indicates that the phospho-mimetic forms of the Wag31 polymers are on average more compact than their phospho-ablative counterparts, which is likely due to the extent of bending/branching. Observed structural features in this first view of Wag31 filaments suggest a basis for higher order Wag31 scaffold formation at the pole.
Collapse
Affiliation(s)
- Komal Choukate
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Aanchal Gupta
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Brohmomoy Basu
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Karman Virk
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Munia Ganguli
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Barnali Chaudhuri
- CSIR Institute of Microbial Technology, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India.
| |
Collapse
|
610
|
Herrera MG, Gómez Castro MF, Prieto E, Barrera E, Dodero VI, Pantano S, Chirdo F. Structural conformation and self-assembly process of p31-43 gliadin peptide in aqueous solution. Implications for celiac disease. FEBS J 2019; 287:2134-2149. [PMID: 31659864 DOI: 10.1111/febs.15109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022]
Abstract
Celiac disease (CeD) is a highly prevalent chronic immune-mediated enteropathy developed in genetically predisposed individuals after ingestion of a group of wheat proteins (called gliadins and glutenins). The 13mer α-gliadin peptide, p31-43, induces proinflammatory responses, observed by in vitro assays and animal models, that may contribute to innate immune mechanisms of CeD pathogenesis. Since a cellular receptor for p31-43 has not been identified, this raises the question of whether this peptide could mediate different biological effects. In this work, we aimed to characterize the p31-43 secondary structure by different biophysical and in silico techniques. By dynamic light scattering and using an oligomer/fibril-sensitive fluorescent probe, we showed the presence of oligomers of this peptide in solution. Furthermore, atomic force microscopy analysis showed p31-43 oligomers with different height distribution. Also, peptide concentration had a very strong influence on peptide self-organization process. Oligomers gradually increased their size at lower concentration. Whereas, at higher ones, oligomers increased their complexity, forming branched structures. By CD, we observed that p31-43 self-organized in a polyproline II conformation in equilibrium with β-sheets-like structures, whose pH remained stable in the range of 3-8. In addition, these findings were supported by molecular dynamics simulation. The formation of p31-43 nanostructures with increased β-sheet structure may help to explain the molecular etiopathogenesis in the induction of proinflammatory effects and subsequent damage at the intestinal mucosa in CeD.
Collapse
Affiliation(s)
- María Georgina Herrera
- Instituto de Química y Fisicoquímica Biológicas - IQUIFIB (UBA-CONICET), Buenos Aires, Argentina
| | | | - Eduardo Prieto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP-CONICET), La Plata, Argentina
| | | | | | - Sergio Pantano
- Institut Pasteur de Montevideo, Uruguay.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, China
| | - Fernando Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, UNLP-CONICET), La Plata, Argentina
| |
Collapse
|
611
|
Xie F, Zan Y, Zhang Y, Zheng N, Yan Q, Zhang W, Zhang H, Jin M, Chen F, Zhang X, Liu S. The cysteine protease ApdS from Streptococcus suis promotes evasion of innate immune defenses by cleaving the antimicrobial peptide cathelicidin LL-37. J Biol Chem 2019; 294:17962-17977. [PMID: 31619521 PMCID: PMC6879338 DOI: 10.1074/jbc.ra119.009441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
Streptococcus suis is a globally distributed zoonotic pathogen associated with meningitis and septicemia in humans, posing a serious threat to public health. To successfully invade and disseminate within its host, this bacterium must overcome the innate immune system. The antimicrobial peptide LL-37 impedes invading pathogens by directly perforating bacterial membranes and stimulating the immune function of neutrophils, which are the major effector cells against S. suis However, little is known about the biological relationship between S. suis and LL-37 and how this bacterium adapts to and evades LL-37-mediated immune responses. In this study by using an array of approaches, including enzyme, chemotaxis, cytokine assays, quantitative RT-PCR, and CD spectroscopy, we found that the cysteine protease ApdS from S. suis cleaves LL-37 and thereby plays a key role in the interaction between S. suis and human neutrophils. S. suis infection stimulated LL-37 production in human neutrophils, and S. suis exposure to LL-37 up-regulated ApdS protease expression in the bacterium. We observed that ApdS targets and rapidly cleaves LL-37, impairing its bactericidal activity against S. suis We attributed this effect to the decreased helical content of the secondary structure in the truncated peptide. Moreover, ApdS rescued S. suis from killing by human neutrophils and neutrophil extracellular traps because LL-37 truncation attenuated neutrophil chemotaxis and inhibited the formation of extracellular traps and the production of reactive oxygen species. Altogether, our findings reveal an immunosuppressive strategy of S. suis whereby the bacterium blunts the innate host defenses via ApdS protease-mediated LL-37 cleavage.
Collapse
Affiliation(s)
- Fang Xie
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yanan Zan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yueling Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Ning Zheng
- First Affiliated Hospital of Dalian Medical University, 116044 Dalian, China
| | - Qiulong Yan
- College of Basic Medical Science, Dalian Medical University, 116044 Dalian, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Huihui Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mingjie Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Fuguang Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinyuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Veterinary Medicine, Inner Mongolia Agricultural University, 010018 Huhehaote, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| |
Collapse
|
612
|
Chen YT, Hu KW, Huang BJ, Lai CH, Tu LH. Inhibiting Human Calcitonin Fibril Formation with Its Most Relevant Aggregation-Resistant Analog. J Phys Chem B 2019; 123:10171-10180. [PMID: 31692350 DOI: 10.1021/acs.jpcb.9b08514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The most common obstacles to the development of therapeutic polypeptides are peptide stability and aggregation. Human calcitonin (hCT) is a 32-residue hormone polypeptide secreted from the C-cells of the thyroid gland and is responsible for calcium and phosphate regulation in the blood. hCT reduces calcium levels by inhibiting the activity of osteoclasts, which are bone cells that are mainly responsible for breaking down the bone tissue or decreasing the resorption of calcium from the kidneys. Thus, calcitonin injection has been used to treat osteoporosis and Paget's disease of bone. hCT is an aggregation-prone peptide with a high tendency to form amyloid fibrils. As a result, salmon calcitonin (sCT), which is different from hCT at 16-residue positions and has a lower propensity to aggregate, has been chosen as a clinical substitute for hCT. However, significant side effects, including immune reactions, have been shown with the use of sCT injection. In this study, we found that two residues, Tyr-12 and Asn-17, play key roles in inducing the fibrillization of hCT. Double mutation of hCT at these two crucial sites could greatly enhance its resistance to aggregation and provide a peptide-based inhibitor to prevent amyloid formation by hCT. Double-mutated hCT retains its ability to interact with its receptor in vivo. These findings suggest that this variant of hCT would serve as a valuable therapeutic alternative to sCT.
Collapse
Affiliation(s)
- Yi-Ting Chen
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| | - Kai-Wei Hu
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| | - Bo-Jie Huang
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan
| | - Chian-Hui Lai
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan
| | - Ling-Hsien Tu
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| |
Collapse
|
613
|
Chaudhary H, Fernandes RMF, Gowda V, Claessens MMAE, Furó I, Lendel C. Intrinsically disordered protein as carbon nanotube dispersant: How dynamic interactions lead to excellent colloidal stability. J Colloid Interface Sci 2019; 556:172-179. [PMID: 31445446 DOI: 10.1016/j.jcis.2019.08.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 11/19/2022]
Abstract
The rich pool of protein conformations combined with the dimensions and properties of carbon nanotubes create new possibilities in functional materials and nanomedicine. Here, the intrinsically disordered protein α-synuclein is explored as a dispersant of single-walled carbon nanotubes (SWNTs) in water. We use a range of spectroscopic methods to quantify the amount of dispersed SWNT and to elucidate the binding mode of α-synuclein to SWNT. The dispersion ability of α-synuclein is good even with mild sonication and the obtained dispersion is very stable over time. The whole polypeptide chain is involved in the interaction accompanied by a fraction of the chain changing into a helical structure upon binding. Similar to other dispersants, we observe that only a small fraction (15-20%) of α-synuclein is adsorbed on the SWNT surface with an average residence time below 10 ms.
Collapse
Affiliation(s)
- Himanshu Chaudhary
- Department of Chemistry, Division of Applied Physical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden.
| | - Ricardo M F Fernandes
- Department of Chemistry, Division of Applied Physical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden; Centro de Investigação em Química, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, s/n, P-4169-007 Porto, Portugal.
| | - Vasantha Gowda
- Department of Chemistry, Division of Applied Physical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Mireille M A E Claessens
- MESA + Institute for Nanotechnology and Mira Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500AE Enschede, the Netherlands
| | - István Furó
- Department of Chemistry, Division of Applied Physical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Christofer Lendel
- Department of Chemistry, Division of Applied Physical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden.
| |
Collapse
|
614
|
Tavares D, Reimer A, Roy S, Joublin A, Sentchilo V, van der Meer JR. Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol. Sci Rep 2019; 9:16940. [PMID: 31729460 PMCID: PMC6858440 DOI: 10.1038/s41598-019-53507-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/31/2019] [Indexed: 01/24/2023] Open
Abstract
Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here the Escherichia coli RbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in an E. coli reporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2-1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.
Collapse
Affiliation(s)
- Diogo Tavares
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Artur Reimer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
- Novartis, 4056, Basel, Switzerland
| | - Shantanu Roy
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Aurélie Joublin
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
| |
Collapse
|
615
|
Smith PT, Narupai B, Tsui JH, Millik SC, Shafranek RT, Kim DH, Nelson A. Additive Manufacturing of Bovine Serum Albumin-Based Hydrogels and Bioplastics. Biomacromolecules 2019; 21:484-492. [DOI: 10.1021/acs.biomac.9b01236] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patrick T. Smith
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Benjaporn Narupai
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan H. Tsui
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - S. Cem Millik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan T. Shafranek
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Deok-Ho Kim
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Alshakim Nelson
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
616
|
Wang Y, Dong J, Wang Z, Zhou S, Wang Q, Han Q, Gao W, Ren K, Qi J. Strong circular dichroism enhancement by plasmonic coupling between graphene and h-shaped chiral nanostructure. OPTICS EXPRESS 2019; 27:33869-33879. [PMID: 31878446 DOI: 10.1364/oe.27.033869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Circular dichroism (CD) is useful in polarization conversion, negative refraction chemical analysis, and bio-sensing. To achieve strong CD signals, researchers constantly break the symmetry of nanostructures. However, how to further enhance the CD based on a new mechanism has become a new challenge in this field. In this work, a hybrid plasmonic chiral system composed of an array of graphene ribbons (GRs) over h-shaped sliver chiral nanostructures (HSCNs) is theoretically investigated. Results demonstrate that the plasmonic coupling between HSCNs and GRs results in different enhanced absorptions for different circularly polarized lights. The absorbance of right circularly polarized light is enhanced to perfect absorption; the absorption of left circularly polarized light is enhanced weakly. It leads to the CD effect of HSCNs@GRs approaching 88%. The loss distributions of HSCNs and HSCNs@GRs reveal that the absorption is enhanced and transferred from HSCNs to GRs. Moreover, the current distributions of HSCNs@GRs are simplified to equivalent LC resonant circuits, which can qualitatively explain the change of CD signals by tuning geometrical parameters of HSCNs@GRs. The findings of this work provide a new method of enhancing chirality and benefit the design of graphene-based chiral optoelectronic devices.
Collapse
|
617
|
Zurlo E, Gorroño Bikandi I, Meeuwenoord NJ, Filippov DV, Huber M. Tracking amyloid oligomerization with monomer resolution using a 13-amino acid peptide with a backbone-fixed spin label. Phys Chem Chem Phys 2019; 21:25187-25195. [PMID: 31696167 DOI: 10.1039/c9cp01060b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid oligomers are suspected as toxic agents in neurodegenerative disease, and are transient and often heterogeneous, making them difficult to detect. Here we show an approach to track the development of amyloid oligomers in situ by room temperature, continuous wave (cw) 9 and 95 GHz EPR. Three amyloid peptides with the 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid (TOAC) spin label were synthesized by solid phase peptide synthesis: T0EZ (TKVKVLGDVIEVGG) with TOAC (T) at the N-terminus, T5EZ with TOAC in the middle (KVKVTGDVIEVG) and T12EZ with TOAC at the C-terminus (KVKVLGDVIEVTG). These sequences are derived from the K11V (KVKVLGDVIEV) amyloid peptide, which self-aggregates to oligomers with a β-sheet configuration (A. Laganowsky, et al., Science, 2012, 335, 1228-1231). To monitor oligomerization, the rotational correlation time (τr) is measured by cw-EPR. For the backbone-fixed TOAC label that is devoid of local mobility τr should reflect the rotation and thereby the size of the peptide, resp. oligomer. For T5EZ a good match between the measured τr and the size of the peptide is obtained, showing the validity of the approach. One of the three peptides (T0EZ) aggregates (circular dichroism), whereas the other two do not. Since also the respective MTSL (S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate) labelled peptides fail to aggregate, molecular crowding due to the label, rather than the helix-inducing properties of TOAC, seems to be responsible. Following in situ oligomer formation of T0EZ by the change in rotational correlation time, two oligomers are observed, a 5-6 mer and a 15-18 mer. The EPR approach, particularly 95 GHz EPR, enables following oligomerization of one monomer at a time, suggesting that the cw-EPR approach presented is a novel tool to follow amyloid oligomerization with high resolution.
Collapse
Affiliation(s)
- E Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - I Gorroño Bikandi
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - N J Meeuwenoord
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - D V Filippov
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - M Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| |
Collapse
|
618
|
Rogers DM, Jasim SB, Dyer NT, Auvray F, Réfrégiers M, Hirst JD. Electronic Circular Dichroism Spectroscopy of Proteins. Chem 2019. [DOI: 10.1016/j.chempr.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
619
|
Chabrol E, Stojko J, Nicolas A, Botzanowski T, Fould B, Antoine M, Cianférani S, Ferry G, Boutin JA. VHH characterization.Recombinant VHHs: Production, characterization and affinity. Anal Biochem 2019; 589:113491. [PMID: 31676284 DOI: 10.1016/j.ab.2019.113491] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
Among the biological approaches to therapeutics, are the cells, such as CAR-T cells engineered or not, the antibodies armed or not, and the smaller protein scaffolds that can be modified to render them specific of other proteins, à la façon of antibodies. For several years, we explored ways to substitute antibodies by nanobodies (also known as VHHs), the smallest recognizing part of camelids' heavy-chain antibodies: production of those small proteins in host microorganisms, minute analyses, characterization, and qualification of their affinity towards designed targets. Here, we present three standard VHHs described in the literature: anti-albumin, anti-EGF receptor and anti-HER2, a typical cancer cell surface -associated protein. Because they differ slightly in global structure, they are good models to assess our body of analytical methodologies. The VHHs were expressed in several bacteria strains in order to identify and overcome the bottlenecks to obtain homogeneous preparations of this protein. A large panel of biophysical tools, ranging from spectroscopy to mass spectrometry, was here combined to assess VHH structural features and the impact of the disulfide bond. The routes are now ready to move to more complex VHHs raised against specific targets in numerous areas including oncology.
Collapse
Affiliation(s)
- Eric Chabrol
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Johann Stojko
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Alexandre Nicolas
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, 67000, Strasbourg, France
| | - Benjamin Fould
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Mathias Antoine
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, 67000, Strasbourg, France
| | - Gilles Ferry
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France.
| | - Jean A Boutin
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France; Institut de Recherches Internationales Servier, 50 rue Carnot, 92284, Suresnes Cedex, France.
| |
Collapse
|
620
|
Suresh V, Sundaram R, Dash P, Sabat SC, Mohapatra D, Mohanty S, Vasudevan D, Senapati S. Macrophage migration inhibitory factor of Syrian golden hamster shares structural and functional similarity with human counterpart and promotes pancreatic cancer. Sci Rep 2019; 9:15507. [PMID: 31664114 PMCID: PMC6820718 DOI: 10.1038/s41598-019-51947-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases. Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions, the information obtained from these models is biased towards a specific species. In experimental science, results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans. Syrian golden hamster (Mesocricetus auratus), is a clinically relevant animal model for multiple human diseases. Hence, the major objectives of this study were to characterize the structure and function of Mesocricetus auratus MIF (MaMIF) and finally evaluate its effect on pancreatic tumor growth in vivo. Initially, the recombinant MaMIF was cloned, expressed and purified in a bacterial expression system. The MaMIF primary sequence, biochemical properties, and crystal structure analysis showed greater similarity with human MIF. The crystal structure of MaMIF illustrates that it forms a homotrimer as known in human and mouse. However, MaMIF exhibits some minor structural variations when compared to human and mouse MIF. The in vitro functional studies show that MaMIF has tautomerase activity and enhances activation and migration of hamster peripheral blood mononuclear cells (PBMCs). Interestingly, injection of MaMIF into HapT1 pancreatic tumor-bearing hamsters significantly enhanced the tumor growth and tumor-associated angiogenesis. Together, the current study shows a structural and functional similarity between the hamster and human MIF. Moreover, it has demonstrated that a high level of circulating MIF originating from non-tumor cells might also promote pancreatic tumor growth in vivo.
Collapse
Affiliation(s)
- Voddu Suresh
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rajivgandhi Sundaram
- Macromolecular Crystallography Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Pujarini Dash
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Surendra Chandra Sabat
- Molecular Biology of Abiotic Stress Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Debasish Mohapatra
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sneha Mohanty
- Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Dileep Vasudevan
- Macromolecular Crystallography Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Shantibhusan Senapati
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| |
Collapse
|
621
|
SERF engages in a fuzzy complex that accelerates primary nucleation of amyloid proteins. Proc Natl Acad Sci U S A 2019; 116:23040-23049. [PMID: 31659041 DOI: 10.1073/pnas.1913316116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The assembly of small disordered proteins into highly ordered amyloid fibrils in Alzheimer's and Parkinson's patients is closely associated with dementia and neurodegeneration. Understanding the process of amyloid formation is thus crucial in the development of effective treatments for these devastating neurodegenerative diseases. Recently, a tiny, highly conserved and disordered protein called SERF was discovered to modify amyloid formation in Caenorhabditis elegans and humans. Here, we use kinetics measurements and native ion mobility-mass spectrometry to show that SERF mainly affects the rate of primary nucleation in amyloid formation for the disease-related proteins Aβ40 and α-synuclein. SERF's high degree of plasticity enables it to bind various conformations of monomeric Aβ40 and α-synuclein to form structurally diverse, fuzzy complexes. This structural diversity persists into early stages of amyloid formation. Our results suggest that amyloid nucleation is considerably more complex than age-related conversion of Aβ40 and α-synuclein into single amyloid-prone conformations.
Collapse
|
622
|
Insight into the Structure of the "Unstructured" Tau Protein. Structure 2019; 27:1710-1715.e4. [PMID: 31628033 DOI: 10.1016/j.str.2019.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/02/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Combining structural proteomics experimental data with computational methods is a powerful tool for protein structure prediction. Here, we apply a recently developed approach for de novo protein structure determination based on the incorporation of short-distance crosslinking data as constraints in discrete molecular dynamics simulations (CL-DMD), for the determination of the conformational ensemble of tau protein in solution. The predicted structures were in agreement with surface modification and long-distance crosslinking data. Tau in solution was found as an ensemble of rather compact globular conformations with distinct topology, inter-residue contacts, and a number of transient secondary-structure elements. Regions important for pathological aggregation consistently were found to contain β strands. The determined structures are compatible with the tau protein in solution being a molten globule at near-ground state with persistent residual structural features which we were able to capture by CL-DMD. The predicted structure may facilitate an understanding of the misfolding and oligomerization pathways of the tau protein.
Collapse
|
623
|
Shukla N, Goeks J, Taylor EA, Othon CM. Hydration Dynamics in Solutions of Cyclic Polyhydroxyl Osmolytes. J Phys Chem B 2019; 123:8472-8479. [PMID: 31508961 DOI: 10.1021/acs.jpcb.9b06861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Simple sugars are remarkably effective at preserving protein and enzymatic structures against thermal and hydrostatic stress. Here, we investigate the hydrodynamic and biopreservative properties of three small cyclic molecules: glucose, myo-inositol, and methyl-α-d-glucopyranoside using circular dichroism spectroscopy and isothermal calorimetry. Using ultrafast fluorescence frequency upconversion spectroscopy, we measure the dynamical retardation of hydration dynamics in cosolute solutions. We find that all three molecules are effective modifiers of hydration dynamics in solution and all are also effective at protecting model protein systems against thermal denaturation. Methyl-α-d-glucopyranoside is found to be the most effective dynamic reducer displaying an approximately 30% increase in solvation relaxation time as compared to water in a cosolute free solution. myo-Inositol and glucose both exhibit a smaller reduction in dynamics with similar magnitudes of concentration dependence. Using these cosolute models, we demonstrate that the thermal enhancement of protein structure does not correlate strongly with either the dynamical reduction of the bulk solution nor with the number of hydrogen bonds a cosolute makes with the solvent. Furthermore, solutions of glucose at twice the concentration of trehalose are shown to have similar magnitudes of dynamical impact. This implies that regulation of hydration dynamics is not a distinguishing characteristic of successful osmolytes. This work highlights the need for further studies and computational analysis to understand the phenomena of preferential exclusion and the contribution of hydration dynamics to protein structural stability.
Collapse
Affiliation(s)
| | - Julia Goeks
- Department of Physics , Ripon College , Ripon , Wisconsin 54971 , United States
| | | | - Christina M Othon
- Department of Physics , Ripon College , Ripon , Wisconsin 54971 , United States
| |
Collapse
|
624
|
Shi Y, Ferreira DS, Banerjee J, Pickford AR, Azevedo HS. Tuning the matrix metalloproteinase-1 degradability of peptide amphiphile nanofibers through supramolecular engineering. Biomater Sci 2019; 7:5132-5142. [PMID: 31576824 DOI: 10.1039/c9bm00949c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Matrix metalloproteinases (MMPs) are a family of endopeptidases capable of degrading extracellular matrix (ECM) components. They are known to play crucial roles during the ECM turnover in both physiological and pathological processes. As such, their activities are utilized as biological stimuli to engineer MMP-responsive peptide-based biomaterials such as self-assembled peptide amphiphiles (PAs). Although previous studies have unveiled the role of PAs secondary structure on the mechanical and biological properties of their self-assembled nanostructures, the effect on the degradability of their assemblies by MMP-1 has not been reported. Herein, a series of PAs are designed and synthesized, all comprising the same MMP-1 cleavable domain but with variable structural segments, to decipher the role of PA's secondary structure on the MMP-1 degradability of their assemblies. This study reveals a correlation between the MMP-1 degradation efficiency and the β-sheet content of the self-assembled PA nanofibers, with the MMP-1 cleavability being significantly reduced in the PA nanofibers with stronger β-sheet characteristics. These results shed light on the role of supramolecular cohesion in PA assemblies on their hydrolysis by MMP-1 and open up the possibility to control the degradation rate of PA-based nanostructures by MMP-1 through tweaking their molecular sequences.
Collapse
Affiliation(s)
- Yejiao Shi
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary, University of London, E1 4NS, UK.
| | - Daniela S Ferreira
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary, University of London, E1 4NS, UK.
| | - Jayati Banerjee
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary, University of London, E1 4NS, UK.
| | - Andrew R Pickford
- Centre for Enzyme Innovation & School of Biological Sciences, University of Portsmouth, PO1 2DY, UK
| | - Helena S Azevedo
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary, University of London, E1 4NS, UK.
| |
Collapse
|
625
|
Wisdom EC, Zhou Y, Chen C, Tamerler C, Snead ML. Mitigation of peri-implantitis by rational design of bifunctional peptides with antimicrobial properties. ACS Biomater Sci Eng 2019; 6:2682-2695. [PMID: 32467858 DOI: 10.1021/acsbiomaterials.9b01213] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The integration of molecular and cell biology with materials science has led to strategies to improve the interface between dental implants with the surrounding soft and hard tissues in order to replace missing teeth and restore mastication. More than 3 million implants have been placed in the US alone and this number is rising by 500,000/year. Peri-implantitis, an inflammatory response to oral pathogens growing on the implant surface threatens to reduce service life leading to eventual implant failure, and such an outcome will have adverse impact on public health and create significant health care costs. Here we report a predictive approach to peptide design, which enabled us to engineer a bifunctional peptide to combat bacterial colonization and biofilm formation, reducing the adverse host inflammatory immune response that destroys the tissue surrounding implants and shortens their lifespans. This bifunctional peptide contains a titanium-binding domain that recognizes and binds with high affinity to titanium implant surfaces, fused through a rigid spacer domain with an antimicrobial domain. By varying the antimicrobial peptide domain, we were able to predict the properties of the resulting bifunctional peptides in their entirety by analyzing the sequence-structure-function relationship. These bifunctional peptides achieve: 1) nearly 100% surface coverage within minutes, a timeframe suitable for their clinical application to existing implants; 2) nearly 100% binding to a titanium surface even in the presence of contaminating serum protein; 3) durability to brushing with a commercially available electric toothbrush; and 4) retention of antimicrobial activity on the implant surface following bacterial challenge. A bifunctional peptide film can be applied to both new implants and/or repeatedly applied to previously placed implants to control bacterial colonization mitigating peri-implant disease that threatens dental implant longevity.
Collapse
Affiliation(s)
- E Cate Wisdom
- Bioengineering Program, Institute for Bioengineering Research, University of Kansas, Lawrence, USA
| | - Yan Zhou
- Herman Ostrow School of Dentistry of USC, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, USA
| | - Casey Chen
- Herman Ostrow School of Dentistry of USC, Division of Periodontology, Diagnostic Services, & Dental Hygiene University of Southern California, Los Angeles, USA
| | - Candan Tamerler
- Bioengineering Program, Institute for Bioengineering Research, University of Kansas, Lawrence, USA.,Mechanical Engineering Department, University of Kansas, Lawrence, USA
| | - Malcolm L Snead
- Herman Ostrow School of Dentistry of USC, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, USA
| |
Collapse
|
626
|
Sahli L, Renard D, Solé-Jamault V, Giuliani A, Boire A. Role of protein conformation and weak interactions on γ-gliadin liquid-liquid phase separation. Sci Rep 2019; 9:13391. [PMID: 31527735 PMCID: PMC6746847 DOI: 10.1038/s41598-019-49745-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023] Open
Abstract
Wheat storage proteins, gliadins, were found to form in vitro condensates in 55% ethanol/water mixture by decreasing temperature. The possible role of this liquid-liquid phase separation (LLPS) process on the in vivo gliadins storage is elusive and remains to be explored. Here we use γ-gliadin as a model of wheat proteins to probe gliadins behavior in conditions near physiological conditions. Bioinformatic analyses suggest that γ-gliadin is a hybrid protein with N-terminal domain predicted to be disordered and C-terminal domain predicted to be ordered. Spectroscopic data highlight the disordered nature of γ-gliadin. We developed an in vitro approach consisting to first solubilize γ-gliadin in 55% ethanol (v/v) and to progressively decrease ethanol ratio in favor of increased aqueous solution. Our results show the ability of γ-gliadin to self-assemble into dynamic droplets through LLPS, with saturation concentrations ranging from 25.9 µM ± 0.85 µM (35% ethanol (v/v)) to 3.8 µM ± 0.1 µM (0% ethanol (v/v)). We demonstrate the importance of the predicted ordered C-terminal domain of γ-gliadin in the LLPS by highlighting the protein condensates transition from a liquid to a solid state under reducing conditions. We demonstrate by increasing ionic strength the role displayed by electrostatic interactions in the phase separation. We also show the importance of hydrogen bonds in this process. Finally, we discuss the importance of gliadins condensates in their accumulation and storage in the wheat seed.
Collapse
Affiliation(s)
- Line Sahli
- INRA, UR1268 Biopolymers Interactions Assemblies, 44300, Nantes, France.
| | - Denis Renard
- INRA, UR1268 Biopolymers Interactions Assemblies, 44300, Nantes, France
| | | | - Alexandre Giuliani
- DISCO beamline, Synchrotron Soleil, l'Orme des Merisiers, 91192, Gif sur Yvette, France
- UAR 1008, CEPIA, INRA, BP 71627, F-44316, Nantes, France
| | - Adeline Boire
- INRA, UR1268 Biopolymers Interactions Assemblies, 44300, Nantes, France
| |
Collapse
|
627
|
Simmons JR, Xu L, Rainey JK. Recombinant Pyriform Silk Fiber Mechanics Are Modulated by Wet-Spinning Conditions. ACS Biomater Sci Eng 2019; 5:4985-4993. [DOI: 10.1021/acsbiomaterials.9b00504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
628
|
Kendrick BS, Gabrielson JP, Solsberg CW, Ma E, Wang L. Determining Spectroscopic Quantitation Limits for Misfolded Structures. J Pharm Sci 2019; 109:933-936. [PMID: 31521643 DOI: 10.1016/j.xphs.2019.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022]
Abstract
Protein secondary structures are frequently assessed using infrared and circular dichroism spectroscopies during drug development (e.g., during product comparability and biosimilarity studies, reference standard characterization, etc.) However, there is little information on the lower limits of quantitation of structural misfolds and impurities for these methods. A model system using a monoclonal antibody reference material was spiked at various levels with a protein that had a significantly different secondary structure to represent the presence of a stable and discreet structural misfold. The ability of circular dichroism, transmission Fourier transform infrared spectroscopy and microfluidic modulation spectroscopy, along with various spectral comparison algorithms, were assessed for their ability to detect the presence and quantify the amount of the misfolded structure.
Collapse
Affiliation(s)
| | | | | | - Eugene Ma
- RedShiftBio, Burlington, Massachusetts 01803
| | - Libo Wang
- RedShiftBio, Burlington, Massachusetts 01803
| |
Collapse
|
629
|
Stapelfeldt K, Stamboroski S, Walter I, Suter N, Kowalik T, Michaelis M, Brüggemann D. Controlling the Multiscale Structure of Nanofibrous Fibrinogen Scaffolds for Wound Healing. NANO LETTERS 2019; 19:6554-6563. [PMID: 31418579 DOI: 10.1021/acs.nanolett.9b02798] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a key player in blood coagulation and tissue repair, fibrinogen has gained increasing attention to develop nanofibrous biomaterial scaffolds for wound healing. Current techniques to prepare protein nanofibers, like electrospinning or extrusion, are known to induce lasting changes in the protein conformation. Often, such secondary changes are associated with amyloid transitions, which can evoke unwanted disease mechanisms. Starting from our recently introduced technique to self-assemble fibrinogen scaffolds in physiological salt buffers, we here investigated the morphology and secondary structure of our novel fibrinogen nanofibers. Aiming at optimum self-assembly conditions for wound healing scaffolds, we studied the influence of fibrinogen concentration and pH on the protein conformation. Using circular dichroism and Fourier-transform infrared spectroscopy, we observed partial transitions from α-helical structures to β-strands upon fiber formation. Interestingly, a staining with thioflavin T revealed that this conformational transition was not associated with any amyloid formation. Toward novel scaffolds for wound healing, which are stable in aqueous environment, we also introduced cross-linking of fibrinogen scaffolds in formaldehyde vapor. This treatment allowed us to maintain the nanofibrous morphology while the conformation of fibrinogen nanofibers was redeveloped toward a more native state after rehydration. Altogether, self-assembled fibrinogen scaffolds are excellent candidates for novel wound healing systems since their multiscale structures can be well controlled without inducing any pathogenic amyloid transitions.
Collapse
Affiliation(s)
- Karsten Stapelfeldt
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Stephani Stamboroski
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials , Wiener Strasse 12 , 28359 Bremen , Germany
| | - Irina Walter
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Naiana Suter
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Thomas Kowalik
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials , Wiener Strasse 12 , 28359 Bremen , Germany
| | - Monika Michaelis
- Interdisciplinary Biomedical Research Centre , Nottingham Trent University , Clifton Lane , Nottingham NG11 8NS , U.K
- Hybrid Materials Interfaces Group , University of Bremen , Am Fallturm 1 , 28359 Bremen , Germany
| | - Dorothea Brüggemann
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
- MAPEX Center for Materials and Processes , University of Bremen , 28359 Bremen , Germany
| |
Collapse
|
630
|
Mandal S, Prasad SR, Mandal D, Das P. Bovine Serum Albumin Amplified Reactive Oxygen Species Generation from Anthrarufin-Derived Carbon Dot and Concomitant Nanoassembly for Combination Antibiotic-Photodynamic Therapy Application. ACS APPLIED MATERIALS & INTERFACES 2019; 11:33273-33284. [PMID: 31433943 DOI: 10.1021/acsami.9b12455] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Amplification of reactive oxygen species (ROS) generation through covalent conjugation of bovine serum albumin (BSA) with newly synthesized, ROS-producing carbon dots (CDs) upon visible light irradiation is reported for the first time. Derivatization of surface carboxyl functional groups of Anthrarufin-derived, green-emitting CD with the amine functionality of BSA ushers distinct changes in the photophysics of CD including an unprecedented ∼50 nm shift in its excitation maxima, decrease in fluorescence lifetime, and concomitant increase in ROS generation. Substantial conformational changes of BSA were witnessed upon conjugation with CD, rendering the BSA-CD conjugate resistant to pepsinolysis. A protease-proof nanoassembly was derived from the BSA-CD conjugate through desolvation that simultaneously hosts a prototype antibiotic and generates ROS with excellent efficiency, making it an attractive platform for antibacterial photodynamic therapy (A-PDT) applications. Systemic annihilation of both Gram-positive and -negative bacteria was achieved with the BSA-CD nanoassembly and envisioned as alternatives to traditional photosensitizers.
Collapse
Affiliation(s)
- Saptarshi Mandal
- Department of Chemistry , Indian Institute of Technology Patna , Patna , 801103 Bihar India
| | - Surendra Rajit Prasad
- Department of Biotechnology , National Institute of Pharmaceutical Education and Research (NIPER) , Hajipur , Bihar 844102 , India
| | - Debabrata Mandal
- Department of Biotechnology , National Institute of Pharmaceutical Education and Research (NIPER) , Hajipur , Bihar 844102 , India
| | - Prolay Das
- Department of Chemistry , Indian Institute of Technology Patna , Patna , 801103 Bihar India
| |
Collapse
|
631
|
Polykretis P, Luchinat E, Bonucci A, Giachetti A, Graewert MA, Svergun DI, Banci L. Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach. IUCRJ 2019; 6:948-957. [PMID: 31576227 PMCID: PMC6760453 DOI: 10.1107/s205225251901073x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
The X-chromosome-linked inhibitor of apoptosis protein (XIAP) is a multidomain protein whose main function is to block apoptosis by caspase inhibition. XIAP is also involved in other signalling pathways, including NF-κB activation and copper homeostasis. XIAP is overexpressed in tumours, potentiating cell survival and resistance to chemotherapeutics, and has therefore become an important target for the treatment of malignancy. Despite the fact that the structure of each single domain is known, the conformation of the full-length protein has never been determined. Here, the first structural model of the full-length XIAP dimer, determined by an integrated approach using nuclear magnetic resonance, small-angle X-ray scattering and electron paramagnetic resonance data, is presented. It is shown that XIAP adopts a compact and relatively rigid conformation, implying that the spatial arrangement of its domains must be taken into account when studying the interactions with its physiological partners and in developing effective inhibitors.
Collapse
Affiliation(s)
- Panagis Polykretis
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Luchinat
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences ‘Mario Serio’, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Alessio Bonucci
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Andrea Giachetti
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Melissa A. Graewert
- EMBL, Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- EMBL, Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucia Banci
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
632
|
Lee J, Lee JH, Paik SR, Yeom B, Char K. Thermally triggered self-assembly of κ-casein amyloid nanofibrils and their nanomechanical properties. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
633
|
John T, Dealey TJA, Gray NP, Patil NA, Hossain MA, Abel B, Carver JA, Hong Y, Martin LL. The Kinetics of Amyloid Fibrillar Aggregation of Uperin 3.5 Is Directed by the Peptide’s Secondary Structure. Biochemistry 2019; 58:3656-3668. [DOI: 10.1021/acs.biochem.9b00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten John
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Tiara J. A. Dealey
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nicholas P. Gray
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nitin A. Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - John A. Carver
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Lisandra L. Martin
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
634
|
Viet KK, Wagner A, Schwickert K, Hellwig N, Brennich M, Bader N, Schirmeister T, Morgner N, Schindelin H, Hellmich UA. Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain. Structure 2019; 27:1246-1257.e5. [DOI: 10.1016/j.str.2019.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 11/28/2022]
|
635
|
Sukhanova A, Poly S, Bozrova S, Lambert É, Ewald M, Karaulov A, Molinari M, Nabiev I. Nanoparticles With a Specific Size and Surface Charge Promote Disruption of the Secondary Structure and Amyloid-Like Fibrillation of Human Insulin Under Physiological Conditions. Front Chem 2019; 7:480. [PMID: 31417892 PMCID: PMC6683663 DOI: 10.3389/fchem.2019.00480] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/24/2019] [Indexed: 01/08/2023] Open
Abstract
Nanoparticles attract much interest as fluorescent labels for diagnostic and therapeutic tools, although their applications are often hindered by size- and shape-dependent cytotoxicity. This cytotoxicity is related not only to the leak of toxic metals from nanoparticles into a biological solution, but also to molecular cytotoxicity effects determined by the formation of a protein corona, appearance of an altered protein conformation leading to exposure of cryptic epitopes and cooperative effects involved in the interaction of proteins and peptides with nanoparticles. In the last case, nanoparticles may serve, depending on their nature, as centers of self-association or fibrillation of proteins and peptides, provoking amyloid-like proteinopathies, or as inhibitors of self-association of proteins, or they can self-assemble on biopolymers as on templates. In this study, human insulin protein was used to analyze nanoparticle-induced proteinopathy in physiological conditions. It is known that human insulin may form amyloid fibers, but only under extreme experimental conditions (very low pH and high temperatures). Here, we have shown that the quantum dots (QDs) may induce amyloid-like fibrillation of human insulin under physiological conditions through a complex process strongly dependent on the size and surface charge of QDs. The insulin molecular structure and fibril morphology have been shown to be modified at different stages of its fibrillation, which has been proved by comparative analysis of the data obtained using circular dichroism, dynamic light scattering, amyloid-specific thioflavin T (ThT) assay, transmission electron microscopy, and high-speed atomic force microscopy. We have found important roles of the QD size and surface charge in the destabilization of the insulin structure and the subsequent fibrillation. Remodeling of the insulin secondary structure accompanied by remarkable increase in the rate of formation of amyloid-like fibrils under physiologically normal conditions was observed when the protein was incubated with QDs of exact specific diameter coated with slightly negative specific polyethylene glycol (PEG) derivatives. Strongly negatively or slightly positively charged PEG-modified QDs of the same specific diameter or QDs of bigger or smaller diameters had no effect on insulin fibrillation. The observed effects pave the way to the control of amyloidosis proteinopathy by varying the nanoparticle size and surface charge.
Collapse
Affiliation(s)
- Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France.,Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
| | - Simon Poly
- Department of Membrane Biophysics, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Svetlana Bozrova
- Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
| | - Éléonore Lambert
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Maxime Ewald
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Michael Molinari
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims, France.,Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, Moscow, Russia
| |
Collapse
|
636
|
Michaelis M, Hildebrand N, Meißner RH, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Delle Piane M, Colombi Ciacchi L. Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. J Phys Chem B 2019; 123:6694-6704. [DOI: 10.1021/acs.jpcb.9b03932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- M. Michaelis
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - N. Hildebrand
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - R. H. Meißner
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - N. Wurzler
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Z. Li
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - J. D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - A. Micsonai
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - J. Kardos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - M. Delle Piane
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - L. Colombi Ciacchi
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| |
Collapse
|
637
|
Nickel-Induced Oligomerization of the Histidine-Rich Metallochaperone CooJ from Rhodospirillum Rubrum. INORGANICS 2019. [DOI: 10.3390/inorganics7070084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
[NiFe]-carbon monoxide dehydrogenase reversibly catalyzes the oxidation of CO to CO2. Its active site is a unique NiFe4S4 cluster, known as C-cluster. In Rhodospirillum rubrum, three nickel-dependent proteins, CooC, CooT and CooJ are required for Ni insertion into the active site. Among them, CooJ is a histidine-rich protein, containing two distinct and spatially separated Ni(II)-binding sites: a strictly conserved N-terminal site and a variable histidine tail at the C-terminus. Here, using biophysical techniques, we study the behavior of the protein upon Ni(II) addition. Using circular dichroism and chemical denaturation, we show that the binding of Ni(II) to the protein increases its stability. Moreover, high-order oligomers are formed through nickel–histidine tail interactions, both in vitro and in cellulo, via a dynamical and reversible process.
Collapse
|
638
|
Stachowski T, Grant TD, Snell EH. Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:967-979. [PMID: 31274418 PMCID: PMC6613122 DOI: 10.1107/s1600577519005113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/14/2019] [Indexed: 05/24/2023]
Abstract
Dissociation of transforming growth factor beta-1 (TGFβ-1) from the inhibitory protein latency-associated peptide (LAP) can occur from low doses of X-ray irradiation of the LAP-TGFβ-1 complex, resulting in the activation of TGFβ-1, and can have health-related consequences. Using the tools and knowledge developed in the study of radiation damage in the crystallographic setting, small-angle X-ray scattering (SAXS) and complementary techniques suggest an activation process that is initiated but not driven by the initial X-ray exposure. LAP is revealed to be extended when not bound to TGFβ-1 and has a different structural conformation compared to the bound state. These studies pave the way for the structural understanding of systems impacted at therapeutic X-ray doses and show the potential impact of radiation damage studies beyond their original intent.
Collapse
Affiliation(s)
- Timothy Stachowski
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Thomas D. Grant
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| |
Collapse
|
639
|
Samainukul N, Linn AK, Javadi MB, Sakdee S, Angsuthanasombat C, Katzenmeier G. Importance of the Cys 124-Cys 128 intermolecular disulfide bonding for oligomeric assembly and hemolytic activity of the Helicobacter pylori TlyA hemolysin. Biochem Biophys Res Commun 2019; 514:365-371. [PMID: 31040022 DOI: 10.1016/j.bbrc.2019.04.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/13/2019] [Indexed: 01/16/2023]
Abstract
Although the TlyA hemolysin from Helicobacter pylori has been implicated as a potential virulence factor involved in mediating host cell colonization and hence disease progression, its structural determinants underlying the biological activity are still largely uncertain. In this study, an important role of the formation of a particular disulfide bond for functional oligomeric assembly of the H. pylori TlyA toxin was evidently elucidated. The 27-kDa TlyA recombinant protein was overexpressed in Escherichia coli, subsequently purified to near homogeneity by cation exchange chromatography, and proven to be hemolytically active against sheep erythrocytes. Additionally, TlyA-induced hemolytic activity was significantly diminished under conditions of disulfide bond reduction with a thiol-reducing agent, dithiothreitol. When the purified TlyA protein was subjected to modified SDS-PAGE under non-reducing conditions, the presence of an oligomeric state of this protein was clearly revealed by its apparent molecular mass of ∼48 kDa. Recombinant E. coli cells expressing TlyA also displayed contact-dependent hemolysis of erythrocytes, suggesting TlyA localization at the bacterial outer membrane and thus supporting the formation of disulfide-bonded TlyA. Homology-based modeling and in silico structural assembly analysis of TlyA signified potential intermolecular, rather than intramolecular, disulfide bonding through Cys124 and Cys128. Subsequently, single substitution of either of these Cys residues with Ser severely affected the oligomeric assembly of both TlyA mutants and hence abolished their hemolytic activity. Altogether, our present data provide pivotal evidence that the formation of intermolecular disulfide bonding between Cys124 and Cys128 plays a critical role in structural assembly of a biologically active-TlyA oligomer.
Collapse
Affiliation(s)
- Nitchakan Samainukul
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Aung Khine Linn
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Mohammad Bagher Javadi
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Somsri Sakdee
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Chanan Angsuthanasombat
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand; Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Gerd Katzenmeier
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand.
| |
Collapse
|
640
|
Clark AM, Ponniah K, Warden MS, Raitt EM, Smith BG, Pascal SM. Tetramer formation by the caspase-activated fragment of the Par-4 tumor suppressor. FEBS J 2019; 286:4060-4073. [PMID: 31177609 DOI: 10.1111/febs.14955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/10/2019] [Accepted: 06/06/2019] [Indexed: 11/27/2022]
Abstract
The prostate apoptosis response-4 (Par-4) tumor suppressor can selectively kill cancer cells via apoptosis while leaving healthy cells unharmed. Full length Par-4 has been shown to be predominantly intrinsically disordered in vitro under neutral conditions. As part of the apoptotic process, cellular Par-4 is cleaved at D131 by caspase-3, which generates a 24 kDa C-terminal activated fragment (cl-Par-4) that enters the nucleus and inhibits pro-survival genes, thereby preventing cancer cell proliferation. Here, the structure of cl-Par-4 was investigated using CD spectroscopy, dynamic light scattering, intrinsic tyrosine fluorescence, and size exclusion chromatography with mutli-angle light scattering. Biophysical characterization shows that cl-Par-4 aggregates and is disordered at low ionic strength. However, with increasing ionic strength, cl-Par-4 becomes progressively more helical and less aggregated, ultimately forming largely ordered tetramers at high NaCl concentration. These results, together with previous results showing induced folding at acidic pH, suggest that the in vivo structure and self-association state of cl-Par-4 may be strongly dependent upon cellular environment.
Collapse
Affiliation(s)
- Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Emily M Raitt
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Benjamin G Smith
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| |
Collapse
|
641
|
Sequeira MA, Herrera MG, Dodero VI. Modulating amyloid fibrillation in a minimalist model peptide by intermolecular disulfide chemical reduction. Phys Chem Chem Phys 2019; 21:11916-11923. [PMID: 31125036 DOI: 10.1039/c9cp01846h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptide structural transformation and aggregation is associated with a large number of outsider aetiology diseases, and it is intrinsically linked to amyloid peptide aggregation. Diphenylalanine self-assembled structures are used as robust minimalist beta amyloids not only to elucidate protein aggregation but also to generate hydrogels. Herein, we employed a neutral model peptide Ac-Phe-Phe-Cys-NH2 (Ac-FFC-NH2) to elucidate the role of intermolecular disulfide bonds in protein fibrillation. The Ac-FFC-NH2 peptide initially self-assembles into nanospheres that evolve to amyloid type fibrils under mild oxidative conditions. Incubation of the peptide in the presence of the chemical reduction agent TCEP inhibits the formation of the fibrils, detecting only spherical nanostructures with no secondary structure. Importantly, we triggered the transformation of the preformed linear straight amyloid fibrils to non-fibrillar structures by TCEP treatment. Under this condition, the amyloid bundles are transformed into rings, which evolve to a new spherical microstructure. We showed that the chemical reduction of intermolecular S-S in internal amyloid sequences might favour the off-path intermediates of amyloid fibril growth, even when the fibrils are formed. Our findings demonstrated that in internal amyloid sequences, the formation of intermolecular S-S promotes the formation of amyloid type fibrils; meanwhile, its reduction stabilises non-fibrillar structures. Altogether, this work provides fundamental understanding at the molecular and supramolecular level, thus facilitating the rational design of therapeutic tools for protein aggregation diseases.
Collapse
Affiliation(s)
- María Alejandra Sequeira
- Instituto de Química del Sur (INQUISUR-CONICET), Departamento de Química, Universidad Nacional del Sur, 8000FTN Bahía Blanca, Argentina
| | | | | |
Collapse
|
642
|
V K, I A, HW D, K K. Recombinant expression and purification of a functional bacterial metallo-chaperone PbrD-fusion construct as a potential biosorbent for Pb(II). Protein Expr Purif 2019; 158:27-35. [DOI: 10.1016/j.pep.2019.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/25/2019] [Accepted: 02/11/2019] [Indexed: 01/30/2023]
|
643
|
Hsu YH, Chen YW, Wu MH, Tu LH. Protein Glycation by Glyoxal Promotes Amyloid Formation by Islet Amyloid Polypeptide. Biophys J 2019; 116:2304-2313. [PMID: 31155148 DOI: 10.1016/j.bpj.2019.05.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 04/16/2019] [Accepted: 05/14/2019] [Indexed: 01/01/2023] Open
Abstract
Protein glycation, also known as nonenzymatic glycosylation, is a spontaneous post-translational modification that would change the structure and stability of proteins or hormone peptides. Recent studies have indicated that glycation plays a role in type 2 diabetes (T2D) and neurodegenerative diseases. Over the last two decades, many types of advanced glycation end products (AGEs), formed through the reactions of an amino group of proteins with reducing sugars, have been identified and detected in vivo. However, the effect of glycation on protein aggregation has not been fully investigated. In this study, we aim to elucidate the impact of protein glycation on islet amyloid polypeptide (IAPP, also known as amylin) aggregation, which was strongly associated with T2D. We chemically synthesized glycated IAPP (AGE-IAPP) to mimic the consequence of this hormone peptide in a hyperglycemia (high blood sugar) environment. Our data revealed that AGE-IAPP formed amyloid faster than normal IAPP, and higher-molecular-weight AGE-IAPP oligomers were also observed in the early stage of aggregation. Circular dichroism spectra also indicated that AGE-IAPP exhibited faster conformational changes from random coil to its β-sheet fibrillar states. Moreover, AGE-IAPP can induce normal IAPP to expedite its aggregation process, and its fibrils can also act as templates to promote IAPP aggregation. AGE-IAPP, like normal IAPP, is capable of interacting with synthetic membranes and also exhibits cytotoxicity. Our studies demonstrated that glycation modification of IAPP promotes the amyloidogenic properties of IAPP, and it may play a role in accumulating additional amyloid during T2D progression.
Collapse
Affiliation(s)
- Yi-Hsuan Hsu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Yun-Wen Chen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Hsin Wu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Ling-Hsien Tu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan.
| |
Collapse
|
644
|
Labourel A, Baslé A, Munoz-Munoz J, Ndeh D, Booth S, Nepogodiev SA, Field RA, Cartmell A. Structural and functional analyses of glycoside hydrolase 138 enzymes targeting chain A galacturonic acid in the complex pectin rhamnogalacturonan II. J Biol Chem 2019; 294:7711-7721. [PMID: 30877196 PMCID: PMC6514610 DOI: 10.1074/jbc.ra118.006626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiome. The selection pressures in this environment have spurred the evolution of a complex reservoir of microbial genes encoding carbohydrate-active enzymes (CAZymes). Previously, we have shown that the human gut bacterium Bacteroides thetaiotaomicron (Bt) can depolymerize the most structurally complex glycan, the plant pectin rhamnogalacturonan II (RGII), commonly found in the human diet. Previous investigation of the RGII-degrading apparatus in Bt identified BT0997 as a new CAZyme family, classified as glycoside hydrolase 138 (GH138). The mechanism of substrate recognition by GH138, however, remains unclear. Here, using synthetic substrates and biochemical assays, we show that BT0997 targets the d-galacturonic acid-α-1,2-l-rhamnose linkage in chain A of RGII and that it absolutely requires the presence of a second d-galacturonic acid side chain (linked β-1,3 to l-rhamnose) for activity. NMR analysis revealed that BT0997 operates through a double displacement retaining mechanism. We also report the crystal structure of a BT0997 homolog, BPA0997 from Bacteroides paurosaccharolyticus, in complex with ligands at 1.6 Å resolution. The structure disclosed that the enzyme comprises four domains, including a catalytic TIM (α/β)8 barrel. Characterization of several BT0997 variants identified Glu-294 and Glu-361 as the catalytic acid/base and nucleophile, respectively, and we observed a chloride ion close to the active site. The three-dimensional structure and bioinformatic analysis revealed that two arginines, Arg-332 and Arg-521, are key specificity determinants of BT0997 in targeting d-galacturonic acid residues. In summary, our study reports the first structural and mechanistic analyses of GH138 enzymes.
Collapse
Affiliation(s)
- Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Jose Munoz-Munoz
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Didier Ndeh
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Simon Booth
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| |
Collapse
|
645
|
Chinnathambi S, Karthikeyan S, Hanagata N, Shirahata N. Molecular interaction of silicon quantum dot micelles with plasma proteins: hemoglobin and thrombin. RSC Adv 2019; 9:14928-14936. [PMID: 35516332 PMCID: PMC9064248 DOI: 10.1039/c9ra02829c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/28/2019] [Indexed: 12/03/2022] Open
Abstract
Protein conformational changes are associated with potential cytotoxicity upon interaction with small molecules or nanomaterials. Protein misfolding leads to protein-mediated diseases; thus, it is important to study the conformational changes in proteins using nanoparticles as drug carriers. In this study, the conformational changes in hemoglobin and thrombin were observed using fluorescence spectroscopy, circular dichroism spectroscopy and molecular modelling studies after interaction with non-toxic, water-soluble near-infrared silicon quantum dot micelles. The molecular docking results indicated that the binding affinities of hemoglobin and thrombin with Si QD micelles are good. In addition, molecular dynamics simulations were performed to obtain more detailed information. Overall graphical representation of 1-decene, F-127, and crystal structures of hemoglobin and thrombin.![]()
Collapse
Affiliation(s)
- Shanmugavel Chinnathambi
- International Center for Young Scientists, National Institute for Materials Science (NIMS) 1-2-1 Sengen Tsukuba Ibaraki 305-0047 Japan
| | - Subramani Karthikeyan
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University) MikluhoMaklaya St., 6 Moscow 117198 Russia
| | - Nobutaka Hanagata
- International Center for Materials Nanoarchitectonics (WPI-MANA), NIMS 1-1 Namiki Tsukuba 305-0044 Japan
| | - Naoto Shirahata
- Nanotechnology Innovation Station, NIMS 1-2-1 Sengen Tsukuba Ibaraki 305-0047 Japan
| |
Collapse
|
646
|
Cruz-Gallardo I, Martino L, Kelly G, Atkinson R, Trotta R, De Tito S, Coleman P, Ahdash Z, Gu Y, Bui TTT, Conte MR. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res 2019; 47:4272-4291. [PMID: 30820564 PMCID: PMC6486636 DOI: 10.1093/nar/gkz144] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/22/2022] Open
Abstract
LARP4A belongs to the ancient RNA-binding protein superfamily of La-related proteins (LARPs). In humans, it acts mainly by stabilizing mRNAs, enhancing translation and controlling polyA lengths of heterologous mRNAs. These activities are known to implicate its association with mRNA, protein partners and translating ribosomes, albeit molecular details are missing. Here, we characterize the direct interaction between LARP4A, oligoA RNA and the MLLE domain of the PolyA-binding protein (PABP). Our study shows that LARP4A-oligoA association entails novel RNA recognition features involving the N-terminal region of the protein that exists in a semi-disordered state and lacks any recognizable RNA-binding motif. Against expectations, we show that the La module, the conserved RNA-binding unit across LARPs, is not the principal determinant for oligoA interaction, only contributing to binding to a limited degree. Furthermore, the variant PABP-interacting motif 2 (PAM2w) featured in the N-terminal region of LARP4A was found to be important for both RNA and PABP recognition, revealing a new role for this protein-protein binding motif. Our analysis demonstrates the mutual exclusive nature of the PAM2w-mediated interactions, thereby unveiling a tantalizing interplay between LARP4A, polyA and PABP.
Collapse
Affiliation(s)
- Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Luigi Martino
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Roberta Trotta
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Stefano De Tito
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Pierre Coleman
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Zainab Ahdash
- Department of Chemistry, King’s College London, London SE1 1DB, UK
| | - Yifei Gu
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| |
Collapse
|
647
|
First JT, Webb LJ. Agreement between Experimental and Simulated Circular Dichroic Spectra of a Positively Charged Peptide in Aqueous Solution and on Self-Assembled Monolayers. J Phys Chem B 2019; 123:4512-4526. [DOI: 10.1021/acs.jpcb.9b02102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| |
Collapse
|
648
|
De Bruyn P, Hadži S, Vandervelde A, Konijnenberg A, Prolič-Kalinšek M, Sterckx YGJ, Sobott F, Lah J, Van Melderen L, Loris R. Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7. Biophys J 2019; 116:1420-1431. [PMID: 30979547 DOI: 10.1016/j.bpj.2019.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 11/25/2022] Open
Abstract
PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module's toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Thermal unfolding of PaaR2 is reversible and displays several transitions, suggesting a complex unfolding mechanism. The unfolding data obtained from spectroscopic and calorimetric methods were combined into a unifying thermodynamic model, which suggests a five-state unfolding trajectory. Furthermore, the model allows the calculation of a stability phase diagram, which shows that, under physiological conditions, PaaR2 mainly exists as a dimer that can swiftly oligomerize into an octamer depending on local protein concentrations. These findings, based on a thorough biophysical and thermodynamic analysis of PaaR2, may provide important insights into biological function such as DNA binding and transcriptional regulation.
Collapse
Affiliation(s)
- Pieter De Bruyn
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Alexandra Vandervelde
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium
| | - Maruša Prolič-Kalinšek
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Yann G-J Sterckx
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium; Astbury Centre for Structural Molecular Biology, Leeds, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.
| |
Collapse
|
649
|
Takahara M, Wakabayashi R, Fujimoto N, Minamihata K, Goto M, Kamiya N. Enzymatic Cell‐Surface Decoration with Proteins using Amphiphilic Lipid‐Fused Peptide Substrates. Chemistry 2019; 25:7315-7321. [DOI: 10.1002/chem.201900370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/03/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Mari Takahara
- Department of Materials Science & Chemical EngineeringNational Institute of Technology, Kitakyushu College 5-20-1 Shii, Kokuraminamiku Kitakyushu 802-0985 Japan
| | - Rie Wakabayashi
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Naoki Fujimoto
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Kosuke Minamihata
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Masahiro Goto
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
- Division of Biotechnology, Center for Future ChemistryKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Noriho Kamiya
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
- Division of Biotechnology, Center for Future ChemistryKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| |
Collapse
|
650
|
Thomas S, Liu W, Arora S, Ganesh V, Ko YP, Höök M. The Complex Fibrinogen Interactions of the Staphylococcus aureus Coagulases. Front Cell Infect Microbiol 2019; 9:106. [PMID: 31041195 PMCID: PMC6476931 DOI: 10.3389/fcimb.2019.00106] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022] Open
Abstract
The two coagulases, von Willebrand factor binding protein (vWbp) and Coagulase (Coa), are critical virulence factors in several animal models of invasive Staphylococcus aureus (S. aureus) infections. These proteins are part of an intricate system of proteins that S. aureus uses to assemble a fibrinogen (Fg)/fibrin protective shield surrounding itself. This shield allows the microorganism to evade clearance by the host phagocytic cells. The coagulases can non-proteolytically activate the zymogen prothrombin to convert Fg to fibrin and promote the Fg/fibrin shield formation. The coagulases also bind directly to Fg and the interaction between Coa and Fg has been previously characterized in some detail. However, the mechanism(s) by which vWbp interacts with Fg remains unclear. Here, we show that vWbp and Coa have distinct interactions with Fg, despite being structurally similar. Coa binds with a significantly higher affinity to soluble Fg than to Fg coated on a plastic surface, whereas vWbp demonstrates no preference between the two forms of Fg. The two coagulases appear to target different sites on Fg, as they do not compete with each other in binding to Fg. Similar to Coa, both the N- and C-terminal halves of vWbp (vWbp-N, vWbp-C, respectively) harbor Fg-binding activities. The higher affinity Fg-binding activity resides in vWbp-N; whereas, the C-terminal region of Coa encompasses the major Fg-binding activity. Peptides constituting the previously identified Coa/Efb1 Fg-binding motif fail to inhibit vWbp-C from binding to Fg, indicating that vWbp-C lacks a functional homolog to this motif. Interestingly, the N-terminal prothrombin-binding domains of both coagulases recognize the Fg β-chain, but they appear to interact with different sequence motifs in the host protein. Collectively, our data provide insight into the complex interactions between Fg and the S. aureus coagulases.
Collapse
Affiliation(s)
- Sheila Thomas
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Vannakambodi Ganesh
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Ya-Ping Ko
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Magnus Höök
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| |
Collapse
|