501
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Wien F, Geinguenaud F, Grange W, Arluison V. SRCD and FTIR Spectroscopies to Monitor Protein-Induced Nucleic Acid Remodeling. Methods Mol Biol 2021; 2209:87-108. [PMID: 33201464 DOI: 10.1007/978-1-0716-0935-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies are fast techniques providing important information about the conformation of nucleic acids and proteins. These vibrational and electronic absorption spectroscopies are extremely sensitive to any change in molecular structure. While numerous reviews describe how to analyze DNA structure alone or in the presence of proteins using FTIR and CD, analyses of RNA are scarce. Nevertheless, RNA remodeling proteins are important factors involved in a multitude of roles in the cell. In this chapter, we present applications of synchrotron radiation circular dichroism (SRCD) and FTIR to analyze how proteins may change RNA structure. These include the analysis of RNA melting, or stabilization, of change in helical parameters and base stacking. The effects on the structure of RNA remodeling proteins are also presented.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Frédéric Geinguenaud
- Plateforme CNanoMat, UFR SMBH, Université Paris 13, Bobigny, France.,Inserm, U1148, Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Bobigny, France
| | - Wilfried Grange
- Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS UMR 7504, Strasbourg, France.,Université de Paris, F-75006, Paris, France
| | - Véronique Arluison
- Université de Paris, F-75006, Paris, France. .,Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France.
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502
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Bernardi AV, Gerolamo LE, de Gouvêa PF, Yonamine DK, Pereira LMS, de Oliveira AHC, Uyemura SA, Dinamarco TM. LPMO AfAA9_B and Cellobiohydrolase AfCel6A from A. fumigatus Boost Enzymatic Saccharification Activity of Cellulase Cocktail. Int J Mol Sci 2020; 22:E276. [PMID: 33383972 PMCID: PMC7795096 DOI: 10.3390/ijms22010276] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulose is the most abundant polysaccharide in lignocellulosic biomass, where it is interlinked with lignin and hemicellulose. Bioethanol can be produced from biomass. Since breaking down biomass is difficult, cellulose-active enzymes secreted by filamentous fungi play an important role in degrading recalcitrant lignocellulosic biomass. We characterized a cellobiohydrolase (AfCel6A) and lytic polysaccharide monooxygenase LPMO (AfAA9_B) from Aspergillus fumigatus after they were expressed in Pichia pastoris and purified. The biochemical parameters suggested that the enzymes were stable; the optimal temperature was ~60 °C. Further characterization revealed high turnover numbers (kcat of 147.9 s-1 and 0.64 s-1, respectively). Surprisingly, when combined, AfCel6A and AfAA9_B did not act synergistically. AfCel6A and AfAA9_B association inhibited AfCel6A activity, an outcome that needs to be further investigated. However, AfCel6A or AfAA9_B addition boosted the enzymatic saccharification activity of a cellulase cocktail and the activity of cellulase Af-EGL7. Enzymatic cocktail supplementation with AfCel6A or AfAA9_B boosted the yield of fermentable sugars from complex substrates, especially sugarcane exploded bagasse, by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass.
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Affiliation(s)
- Aline Vianna Bernardi
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Luis Eduardo Gerolamo
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Paula Fagundes de Gouvêa
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Deborah Kimie Yonamine
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Lucas Matheus Soares Pereira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Arthur Henrique Cavalcante de Oliveira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Sérgio Akira Uyemura
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil;
| | - Taisa Magnani Dinamarco
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
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503
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Sinha D, Sinha D, Banerjee N, Rai P, Seal S, Chakraborty T, Chatterjee S, Sau S. A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability. J Biomol Struct Dyn 2020; 40:4972-4986. [PMID: 33356973 DOI: 10.1080/07391102.2020.1864475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RsbW, σB, and RsbV, encoded by Staphylococcus aureus and related bacteria, act as an anti-sigma factor, an sigma factor, and an anti-anti-sigma factor, respectively. The interaction between RsbW and σB blocks the transcription initiation activity of the latter protein. RsbW also functions as a serine kinase and phosphorylates RsbV in the presence of ATP. Our modeling study indicates that the RsbW-RsbV complex is stabilized by twenty-four intermolecular non-covalent bonds. Of the bond-forming RsbW residues, Arg 23, and Glu 49 are conserved residues. To understand the roles of Arg 23 in RsbW, rRsbW[R23A], a recombinant S. aureus RsbW (rRsbW) harboring Arg to Ala change at position 23, was investigated using various probes. The results reveal that rRsbW[R23A], like rRsbW, exists as the dimers in the aqueous solution. However, rRsbW[R23A], unlike rRsbW, neither interacted with a chimeric RsbV (rRsbV) nor formed the phosphorylated rRsbV in the presence of ATP. Furthermore, the tertiary structure and hydrophobic surface area of rRsbW[R23A] matched little with those of rRsbW. Conversely, both rRsbW[R23A] and rRsbW showed interaction with a recombinant σB (rσB). rRsbW and rRsbW[R23A] were also unfolded via the formation of at least one intermediate in the presence of urea. However, the thermodynamic stability of rRsbW significantly differed from that of rRsbW[R23A]. Our molecular dynamics (MD) simulation study also reveals the substantial change of structure, dimension, and stability of RsbW due to the above mutation. The ways side chain of critical Arg 23 contributes to maintaining the tertiary structure, and stability of RsbW was elaborately discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Priya Rai
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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504
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Bostan F, Surmeli NB. Cloning, expression, and characterization of a novel sericin-like protein. Biotechnol Appl Biochem 2020; 69:136-144. [PMID: 33368658 DOI: 10.1002/bab.2089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/13/2020] [Indexed: 11/08/2022]
Abstract
Silk consists of two proteins called fibroin and sericin. While fibroin is used in the textile industry and has various biomaterial applications, sericin has been considered as waste material until recently. Sericin is a multicomponent protein and it has important properties such as biocompatibility, biodegradability, cryoprotectivity, and antioxidant. Sericin from silkworm cocoons can be obtained by chemical, enzymatic, and heat treatment methods. However, sericin obtained with these treatment methods is not of consistent and high quality. Moreover, the exposure of sericin to harsh conditions during extraction leads to inconsistencies in the composition and structure of the sericin obtained. The inconsistencies in sericin structure and composition decrease application of sericin as a biomaterial. Here, we produce a sericin-like protein (Ser4mer) with native sequence of sericin encoding four repeats of the conserved 38 amino acid motif recombinantly in Escherichia coli and characterize its structural properties. Ser4mer protein shows similar structure to native sericin and higher solubility than previously obtained recombinant sericin-like proteins. Recombinant production of a soluble sericin-like protein will significantly expand its applications as a biomaterial. In addition, recombinant production of silk proteins will allow us to understand sequence-structure relationships in these proteins.
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Affiliation(s)
- Fatmanur Bostan
- Program in Biotechnology and Bioengineering, İzmir Institute of Technology, Gülbahce, Urla Izmir, Turkey
| | - Nur Basak Surmeli
- Department of Bioengineering, İzmir Institute of Technology, Gülbahce, Urla Izmir, Turkey
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505
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New RRC, Bui TTT, Bogus M. Binding Interactions of Peptide Aptamers. Molecules 2020; 25:molecules25246055. [PMID: 33371475 PMCID: PMC7767479 DOI: 10.3390/molecules25246055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Affiliation(s)
- Roger R. C. New
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, Hendon, London NW4 4BT, UK
- Correspondence: or
| | - Tam T. T. Bui
- Centre for Biomolecular Spectroscopy and Institute of Pharmaceutical Science, King’s College, London SE1 1UL, UK;
| | - Michal Bogus
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
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506
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Fagerberg E, Månsson LK, Lenton S, Skepö M. The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions. J Phys Chem B 2020; 124:11843-11853. [PMID: 33337879 PMCID: PMC7872433 DOI: 10.1021/acs.jpcb.0c09635] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Intrinsically disordered proteins (IDP) are proteins that sample
a heterogeneous ensemble of conformers in solution. An estimated 25–30%
of all eukaryotic proteins belong to this class. In vivo, IDPs function under conditions that are highly crowded by other
biological macromolecules. Previous research has highlighted that
the presence of crowding agents can influence the conformational ensemble
sampled by IDPs, resulting in either compaction or expansion. The
effects of self-crowding of the disordered protein Histatin 5 has,
in an earlier study, been found to have limited influence on the conformational
ensemble. In this study, it is examined whether the short chain length
of Histatin 5 can explain the limited effects of crowding observed,
by introducing (Histatin 5)2, a tandem repeat of Histatin
5. By utilizing small-angle X-ray scattering, it is shown that the
conformational ensemble is conserved at high protein concentrations,
in resemblance with Histatin 5, although with a lowered protein concentration
at which aggregation arises. Under dilute conditions, atomistic molecular
dynamics and coarse-grained Monte Carlo simulations, as well as an
established scaling law, predicted more extended conformations than
indicated by experimental data, hence implying that (Histatin 5)2 does not behave as a self-avoiding random walk.
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Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | - Linda K Månsson
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | - Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden.,LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden.,LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
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507
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Rani S, Dasgupta B, Bhati GK, Tomar K, Rakshit S, Maiti S. Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media. Chembiochem 2020; 22:1285-1291. [PMID: 33175409 DOI: 10.1002/cbic.202000768] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.
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Affiliation(s)
- Sheetal Rani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Gaurav Kumar Bhati
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Kalpana Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
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508
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Khanna S, Singh AK, Behera SP, Gupta S. Thermoresponsive BSA hydrogels with phase tunability. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111590. [PMID: 33321635 DOI: 10.1016/j.msec.2020.111590] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 12/26/2022]
Abstract
Amyloids are fibrillar structures formed due to protein aggregation or misfolding when the molecules undergo a conformational change from α-helix to β-sheet. Although this self-assembly is associated with many neurodegenerative diseases in vivo, the highly ordered amyloidic structures formed in vitro are ideal scaffolds for many bionanotechnological applications. Amyloid fibrillar networks under specific stimuli can also form stable hydrogels. We have used bovine serum albumin (BSA) as a model amyloidogenic protein to obtain thermally-induced hydrogels that display tunable sol-gel-sol transitions spanning over minutes to days. High concentrations of BSA (14-22% w/v) were heated at 65 °C for less than 3 min without any cross-linking agent to yield soft, injectable gels that were non-toxic to mammalian cells. A detailed investigation of temperature, concentration, incubation time and ionic strength on the formation and reversal of these gels was carried out using visual inspection, rheology, electron microscopy, fluorescence spectroscopy, UV-visible spectroscopy and circular dichroism spectroscopy. The optimum gelation temperature (Tg) for phase reversal of BSA gels was found to lie between 60 and 70 °C. An increase in protein concentration led to a reduction in the gelation time and increase in the gel-to-rev sol transition time. Gels heated for longer duration than their minimum gelation time yielded irreversible gels suggesting that low incubation periods were favourable for partial protein denaturation and hydrogel formation. This was supported by time-resolved secondary and tertiary structural ensemble studies. Further, the hydrogel networks demonstrated a zero-order drug release kinetics and the rev sol was found to be cytocompatible with HaCaT skin cell lines. Overall, our approach demonstrates rapid, crosslinker-free thermoresponsive BSA gelation with wide tunability and control on the time and material property, ideal for topical drug delivery applications.
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Affiliation(s)
- Shruti Khanna
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ajay Kumar Singh
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Soumya Prakash Behera
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shalini Gupta
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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509
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Khrustalev VV, Kordyukova LV, Arutyunyan AM, Poboinev VV, Khrustaleva TA, Stojarov AN, Baratova LA, Sapon AS, Lugin VG. The cytoplasmic tail of influenza A/H1N1 virus hemagglutinin is β-structural. J Biomol Struct Dyn 2020; 40:4642-4661. [PMID: 33317396 DOI: 10.1080/07391102.2020.1860827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Influenza A/H1N1 virus hemagglutinin (HA) is an integral type I glycoprotein that contains a large glycosylated ectodomain, a transmembrane domain, and a cytoplasmic tail (CT) of 10-14 amino acid residues. There are absolutely no data on the secondary or tertiary structure of the HA CT, which is important for virus pathogenesis. Three highly conserved cysteines are post-translationally modified by the attachment of fatty acid residues that pin the CT to the lipid membrane inside the virion. We applied circular dichroism (CD) and fluorescence spectroscopy analysis to examine four synthetic peptides corresponding to 14-15 C-terminal residues of H1 subtype HA (NH2-WMCSNGSLQCRICI-COOH; NH2-FWMCSNGSLQCRICI-COOH), with free or acetaminomethylated cysteines, in the reduced or non-reduced state, at various pH values and temperatures. The CD analysis detected the formation of a β-structure (30-65% according to the new BeStSel algorithm), in addition to an unstructured random coil, in every peptide in various conditions. It was completely or partially recognized as an antiparallel β-structure that was also confirmed by the multi-bounce Horizontal Attenuated Total Reflectance Fourier Transformed Infrared (HATR-FTIR) spectroscopy analysis. According to the experimental data, as well as 3 D modeling, we assume that the amino acid sequence corresponding to the HA CT may form a short antiparallel β-structure under the lipid membrane within a virion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Victor V Poboinev
- Department of General Chemistry, Belarusian State Medical University, Minsk, Belarus
| | - Tatyana A Khrustaleva
- Biochemical group of the Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Aleksander N Stojarov
- Department of Radiation Medicine and Ecology, Belarusian State Medical University, Minsk, Belarus
| | - Lyudmila A Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alena S Sapon
- Center for Physical and Chemical Research Methods, Belarusian State Technological University, Minsk, Belarus
| | - Valery G Lugin
- Center for Physical and Chemical Research Methods, Belarusian State Technological University, Minsk, Belarus
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510
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Sahli L, Boire A, Solé-Jamault V, Rogniaux H, Giuliani A, Roblin P, Renard D. New exploration of the γ-gliadin structure through its partial hydrolysis. Int J Biol Macromol 2020; 165:654-664. [PMID: 32991891 DOI: 10.1016/j.ijbiomac.2020.09.136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 11/25/2022]
Abstract
The partial enzymatic hydrolysis of wheat gliadins constitutes an interesting tool to unravel their structural specificity. In this work, the structure and conformation of γ-gliadin were investigated through its limited chymotrypsic digestion. Using a combination of computational, biochemical and biophysical tools, we studied each of its N and C terminal domains. Our results reveal that γ-gliadin is a partially disordered protein with an unfolded N-terminal domain surprisingly resistant to chymotrypsin and a folded C-terminal domain. Using spectroscopic tools, we showed that structural transitions occured over the disordered N-terminal domain for decreasing ethanol/water ratios. Using SAXS measurements, low-resolution 3D structures of γ-gliadin were proposed. To relate the repeated motifs of the N-terminal domain of γ-gliadin to its structure, engineered peptide models PQQPY/F were also studied. Overall results demonstrated similarities between the N-terminal domain and its derived model peptides. Our findings support the use of these peptides as general templates for understanding the wheat protein assembly and dynamics.
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Affiliation(s)
- Line Sahli
- INRAE, UR1268 Biopolymers Interactions Assemblies, 44300 Nantes, France
| | - Adeline Boire
- INRAE, UR1268 Biopolymers Interactions Assemblies, 44300 Nantes, France
| | | | - Hélène Rogniaux
- INRAE, UR1268 Biopolymers Interactions Assemblies, 44300 Nantes, France; INRAE, BIBS Platform, 44300 Nantes, France
| | - Alexandre Giuliani
- DISCO Beamline, Synchrotron Soleil, l'Orme des Merisiers, 91192 Gif sur Yvette, France; UAR 1008, Transform, INRAE, BP 71627, F-44316, Nantes, France
| | - Pierre Roblin
- Laboratoire de Génie Chimique and Fédération de Recherche FERMAT, 4 allée Emile Monso, 31030 Toulouse, France
| | - Denis Renard
- INRAE, UR1268 Biopolymers Interactions Assemblies, 44300 Nantes, France.
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511
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Narayan G, Sundaravadivelu PK, Agrawal A, Gogoi R, Nagotu S, Thummer RP. Soluble expression, purification, and secondary structure determination of human PDX1 transcription factor. Protein Expr Purif 2020; 180:105807. [PMID: 33309974 DOI: 10.1016/j.pep.2020.105807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/06/2023]
Abstract
The transcription factor PDX1 is a master regulator essential for proper development of the pancreas, duodenum and antrum. Furthermore, it is an indispensable reprogramming factor for the derivation of human β-cells, and recently, it has been identified as a tumor suppressor protein in gastric cancer. Here, we report the soluble expression and purification of the full-length human PDX1 protein from a heterologous system. To achieve this, the 849 bp coding sequence of the PDX1 gene was first codon-optimized for expression in Escherichia coli (E. coli). This codon-optimized gene sequence was fused to a protein transduction domain, a nuclear localization sequence, and a His-tag, and this insert was cloned into the protein expression vector for expression in E. coli strain BL21(DE3). Next, screening and identification of the suitable gene construct and optimal expression conditions to obtain this recombinant fusion protein in a soluble form was performed. Further, we have purified this recombinant fusion protein to homogeneity under native conditions. Importantly, the secondary structure of the protein was retained after purification. Further, this recombinant PDX1 fusion protein was applied to human cells and showed the ability to enter the cells as well as translocate to the nucleus. This recombinant tool can be used as a safe tool and can potentially replace its genetic and viral forms in the reprogramming process to induce a β-cell-specific transcriptional profile in an integration-free manner. Additionally, it can also be used to elucidate its role in cellular processes and for structural and biochemical studies.
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Affiliation(s)
- Gloria Narayan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Akriti Agrawal
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Ranadeep Gogoi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, 781101, Guwahati, Assam, India; CSIR-North East Institute of Science & Technology, Jorhat, 785006, Assam, India.
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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512
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Krenev IA, Umnyakova ES, Eliseev IE, Dubrovskii YA, Gorbunov NP, Pozolotin VA, Komlev AS, Panteleev PV, Balandin SV, Ovchinnikova TV, Shamova OV, Berlov MN. Antimicrobial Peptide Arenicin-1 Derivative Ar-1-(C/A) as Complement System Modulator. Mar Drugs 2020; 18:md18120631. [PMID: 33321960 PMCID: PMC7764584 DOI: 10.3390/md18120631] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
Antimicrobial peptides (AMPs) are not only cytotoxic towards host pathogens or cancer cells but also are able to act as immunomodulators. It was shown that some human and non-human AMPs can interact with complement proteins and thereby modulate complement activity. Thus, AMPs could be considered as the base for complement-targeted therapeutics development. Arenicins from the sea polychaete Arenicola marina, the classical example of peptides with a β-hairpin structure stabilized by a disulfide bond, were shown earlier to be among the most prospective regulators. Here, we investigate the link between arenicins' structure and their antimicrobial, hemolytic and complement-modulating activities using the derivative Ar-1-(C/A) without a disulfide bond. Despite the absence of this bond, the peptide retains all important functional activities and also appears less hemolytic in comparison with the natural forms. These findings could help to investigate new complement drugs for regulation using arenicin derivatives.
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Affiliation(s)
- Ilia A. Krenev
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
- Faculty of Chemistry, Saint Petersburg State University, Universitetskaya Emb, 7/9, 199034 Saint Petersburg, Russia;
| | - Ekaterina S. Umnyakova
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
- Correspondence: ; Tel.: +7-981-971-4975
| | - Igor E. Eliseev
- Nanobiotechnology Laboratory, Alferov University, Khlopin Str. 8/3, 194021 Saint Petersburg, Russia;
| | - Yaroslav A. Dubrovskii
- Faculty of Chemistry, Saint Petersburg State University, Universitetskaya Emb, 7/9, 199034 Saint Petersburg, Russia;
- Almazov National Medical Research Centre, Akkuratov Str, 2, 197341 Saint Petersburg, Russia
| | - Nikolay P. Gorbunov
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
| | - Vladislav A. Pozolotin
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
| | - Alexei S. Komlev
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
| | - Pavel V. Panteleev
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (P.V.P.); (S.V.B.); (T.V.O.)
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (P.V.P.); (S.V.B.); (T.V.O.)
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (P.V.P.); (S.V.B.); (T.V.O.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8-2, 119991 Moscow, Russia
| | - Olga V. Shamova
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
| | - Mikhail N. Berlov
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, Acad. Pavlov Str. 12, 197376 Saint Petersburg, Russia; (I.A.K.); (N.P.G.); (V.A.P.); (A.S.K.); (O.V.S.); (M.N.B.)
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513
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Sajko S, Grishkovskaya I, Kostan J, Graewert M, Setiawan K, Trübestein L, Niedermüller K, Gehin C, Sponga A, Puchinger M, Gavin AC, Leonard TA, Svergun DI, Smith TK, Morriswood B, Djinovic-Carugo K. Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats. PLoS One 2020; 15:e0242677. [PMID: 33296386 PMCID: PMC7725318 DOI: 10.1371/journal.pone.0242677] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/08/2020] [Indexed: 11/19/2022] Open
Abstract
MORN (Membrane Occupation and Recognition Nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. Despite this ubiquity, they remain poorly characterised at both a structural and a functional level compared to other common repeats. In functional terms, they are often assumed to be lipid-binding modules that mediate membrane targeting. We addressed this putative activity by focusing on a protein composed solely of MORN repeats-Trypanosoma brucei MORN1. Surprisingly, no evidence for binding to membranes or lipid vesicles by TbMORN1 could be obtained either in vivo or in vitro. Conversely, TbMORN1 did interact with individual phospholipids. High- and low-resolution structures of the MORN1 protein from Trypanosoma brucei and homologous proteins from the parasites Toxoplasma gondii and Plasmodium falciparum were obtained using a combination of macromolecular crystallography, small-angle X-ray scattering, and electron microscopy. This enabled a first structure-based definition of the MORN repeat itself. Furthermore, all three structures dimerised via their C-termini in an antiparallel configuration. The dimers could form extended or V-shaped quaternary structures depending on the presence of specific interface residues. This work provides a new perspective on MORN repeats, showing that they are protein-protein interaction modules capable of mediating both dimerisation and oligomerisation.
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Affiliation(s)
- Sara Sajko
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Julius Kostan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Kim Setiawan
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Linda Trübestein
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Korbinian Niedermüller
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Charlotte Gehin
- European Molecular Biology Laboratory, Heidelberg Unit, Heidelberg, Germany
- Institute of Bioengineering, Laboratory of Lipid Cell Biology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Antonio Sponga
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Martin Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Heidelberg Unit, Heidelberg, Germany
- Department for Cell Physiology and Metabolism, University of Geneva, Centre Medical Universitaire, Geneva, Switzerland
| | - Thomas A. Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Terry K. Smith
- School of Biology, BSRC, University of St. Andrews, St. Andrews, United Kingdom
| | - Brooke Morriswood
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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514
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Malhotra L, Goyal HKV, Jhuria S, Dev K, Kumar S, Kumar M, Kaur P, Ethayathulla AS. Curcumin rescue p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line: Evidence-based on computational, biophysical, and in vivo studies. Biochim Biophys Acta Gen Subj 2020; 1865:129807. [PMID: 33278547 DOI: 10.1016/j.bbagen.2020.129807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The p53, tumor suppressor protein is inactivated upon mutation in the DNA-binding domain and the non-functional protein leads to cancers. The p53Y220C is one of the most frequently observed mutations in p53 with a scope of rescuing the protein function using small molecules. METHODS Using computational modeling, biophysical, and experimental cell-based studies we tried to understand the molecular basis of Curcumin as a potential small molecule to stabilize p53Y220C mutant and restore its function. The pancreatic adenocarcinomas BxPC-3 p53Y220C mutant cell line was used for cell-based assays to determine the therapeutic potential of Curcumin to restore mutant p53 to function like wild type. RESULTS Our results showed that the Curcumin binds p53Y220C with Kd = 3.169 ± 0.257 μM and it increases the DNA binding affinity of the mutant by 4-fold with Kd = 851.29 ± 186.27 nM. By Fluorescence, CD, and IR spectroscopy, we could characterize the secondary structural changes and stabilization of the p53Y220C DNA binding domain upon Curcumin binding. By caspase-3 and Annexin V assays, we could demonstrate that Curcumin at 3 μM to 8 μM concentration could initiate p53 mediated apoptosis in BxPC-3 cell line. Based on our experimental studies, we propose a mechanism for the activation of ATM/Chk1 kinases pathways for apoptosis and/or G2/M cell cycle arrest in the BxPC-3 cell line mediated by functionally restored p53Y220C. CONCLUSION The study indicated that the natural compound Curcumin could rescue mutant p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line to function like wild-type and activate apoptotic pathways.
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Affiliation(s)
- Lakshay Malhotra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Harsh K V Goyal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sunita Jhuria
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Kapil Dev
- Department of Biotechnology, Jamia Milia Islamia, New Delhi 110025, India
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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515
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Agnolon V, Kiseljak D, Wurm MJ, Wurm FM, Foissard C, Gallais F, Wehrle S, Muñoz-Fontela C, Bellanger L, Correia BE, Corradin G, Spertini F. Designs and Characterization of Subunit Ebola GP Vaccine Candidates: Implications for Immunogenicity. Front Immunol 2020; 11:586595. [PMID: 33250896 PMCID: PMC7672190 DOI: 10.3389/fimmu.2020.586595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
The humoral responses of Ebola virus (EBOV) survivors mainly target the surface glycoprotein GP, and anti-GP neutralizing antibodies have been associated with protection against EBOV infection. In order to elicit protective neutralizing antibodies through vaccination a native-like conformation of the antigen is required. We therefore engineered and expressed in CHO cells several GP variants from EBOV (species Zaire ebolavirus, Mayinga variant), including a soluble GP ΔTM, a mucin-like domain-deleted GP ΔTM-ΔMUC, as well as two GP ΔTM-ΔMUC variants with C-terminal trimerization motifs in order to favor their native trimeric conformation. Inclusion of the trimerization motifs resulted in proteins mimicking GP metastable trimer and showing increased stability. The mucin-like domain appeared not to be critical for the retention of the native conformation of the GP protein, and its removal unmasked several neutralizing epitopes, especially in the trimers. The soluble GP variants inhibited mAbs neutralizing activity in a pseudotype transduction assay, further confirming the proteins' structural integrity. Interestingly, the trimeric GPs, a native-like GP complex, showed stronger affinity for antibodies raised by natural infection in EBOV disease survivors rather than for antibodies raised in volunteers that received the ChAd3-EBOZ vaccine. These results support our hypothesis that neutralizing antibodies are preferentially induced when using a native-like conformation of the GP antigen. The soluble trimeric recombinant GP proteins we developed represent a novel and promising strategy to develop prophylactic vaccines against EBOV and other filoviruses.
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Affiliation(s)
- Valentina Agnolon
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | | | | | - Florian M Wurm
- ExcellGene SA, Monthey, Switzerland.,Faculty of Life Sciences, École Polytechnique Fédérale De Lausanne (EPFL), Lausanne, Switzerland
| | - Charlotte Foissard
- Université Paris Saclay, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- Université Paris Saclay, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale De Lausanne (EPFL), Lausanne, Switzerland
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner site Hamburg, Hamburg, Germany
| | - Laurent Bellanger
- Université Paris Saclay, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Bruno Emanuel Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale De Lausanne (EPFL), Lausanne, Switzerland
| | - Giampietro Corradin
- Department of Biochemistry, Université de Lausanne (UNIL), Epalinges, Switzerland
| | - François Spertini
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
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516
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Characterization of Posttranslationally Modified Multidrug Efflux Pumps Reveals an Unexpected Link between Glycosylation and Antimicrobial Resistance. mBio 2020; 11:mBio.02604-20. [PMID: 33203757 PMCID: PMC7683400 DOI: 10.1128/mbio.02604-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The substantial rise in multidrug-resistant bacterial infections is a current global imperative. Cumulative efforts to characterize antimicrobial resistance in bacteria has demonstrated the spread of six families of multidrug efflux pumps, of which resistance-nodulation-cell division (RND) is the major mechanism of multidrug resistance in Gram-negative bacteria. RND is composed of a tripartite protein assembly and confers resistance to a range of unrelated compounds. In the major enteric pathogen Campylobacter jejuni, the three protein components of RND are posttranslationally modified with N-linked glycans. The direct role of N-linked glycans in C. jejuni and other bacteria has long been elusive. Here, we present the first detailed account of the role of N-linked glycans and the link between N-glycosylation and antimicrobial resistance in C. jejuni We demonstrate the multifunctional role of N-linked glycans in enhancing protein thermostability, stabilizing protein complexes and the promotion of protein-protein interaction, thus mediating antimicrobial resistance via enhancing multidrug efflux pump activity. This affirms that glycosylation is critical for multidrug efflux pump assembly. We present a generalized strategy that could be used to investigate general glycosylation system in Campylobacter genus and a potential target to develop antimicrobials against multidrug-resistant pathogens.IMPORTANCE Nearly all bacterial species have at least a single glycosylation system, but the direct effects of these posttranslational protein modifications are unresolved. Glycoproteome-wide analysis of several bacterial pathogens has revealed general glycan modifications of virulence factors and protein assemblies. Using Campylobacter jejuni as a model organism, we have studied the role of general N-linked glycans in the multidrug efflux pump commonly found in Gram-negative bacteria. We show, for the first time, the direct link between N-linked glycans and multidrug efflux pump activity. At the protein level, we demonstrate that N-linked glycans play a role in enhancing protein thermostability and mediating the assembly of the multidrug efflux pump to promote antimicrobial resistance, highlighting the importance of this posttranslational modification in bacterial physiology. Similar roles for glycans are expected to be found in other Gram-negative pathogens that possess general protein glycosylation systems.
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517
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Nano-Bio Interaction between Blood Plasma Proteins and Water-Soluble Silicon Quantum Dots with Enabled Cellular Uptake and Minimal Cytotoxicity. NANOMATERIALS 2020; 10:nano10112250. [PMID: 33202926 PMCID: PMC7696914 DOI: 10.3390/nano10112250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 01/25/2023]
Abstract
A better understanding of the compatibility of water-soluble semiconductor quantum dots (QDs) upon contact with the bloodstream is important for biological applications, including biomarkers working in the first therapeutic spectral window for deep tissue imaging. Herein, we investigated the conformational changes of blood plasma proteins during the interaction with near-infrared light-emitting nanoparticles, consisting of Pluronic F127 shells and cores comprised of assembled silicon QDs terminated with decane monolayers. Albumin and transferrin have high quenching constants and form a hard protein corona on the nanoparticle. In contrast, fibrinogen has low quenching constants and forms a soft protein corona. A circular dichroism (CD) spectrometric study investigates changes in the protein’s secondary and tertiary structures with incremental changes in the nanoparticle concentrations. As expected, the addition of nanoparticles causes the denaturation of the plasma proteins. However, it is noteworthy that the conformational recovery phenomena are observed for fibrinogen and transferrin, suggesting that the nanoparticle does not influence the ordered structure of proteins in the bloodstream. In addition, we observed enabled cellular uptake (NIH3T3 Fibroblasts) and minimal cytotoxicity using different cell lines (HeLa, A549, and NIH3T3). This study offers a basis to design QDs without altering the biomacromolecule’s original conformation with enabled cellular uptake with minimal cytotoxicity.
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518
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Hyatt JG, Prévost S, Devos JM, Mycroft-West CJ, Skidmore MA, Winter A. Molecular Changes in Dengue Envelope Protein Domain III upon Interaction with Glycosaminoglycans. Pathogens 2020; 9:pathogens9110935. [PMID: 33187224 PMCID: PMC7697694 DOI: 10.3390/pathogens9110935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 11/16/2022] Open
Abstract
Dengue fever is a rapidly emerging vector-borne viral disease with a growing global burden of approximately 390 million new infections per annum. The Dengue virus (DENV) is a flavivirus spread by female mosquitos of the aedes genus, but the mechanism of viral endocytosis is poorly understood at a molecular level, preventing the development of effective transmission blocking vaccines (TBVs). Recently, glycosaminoglycans (GAGs) have been identified as playing a role during initial viral attachment through interaction with the third domain of the viral envelope protein (EDIII). Here, we report a systematic study investigating the effect of a range of biologically relevant GAGs on the structure and oligomeric state of recombinantly generated EDIII. We provide novel in situ biophysical evidence that heparin and chondroitin sulphate C induce conformational changes in EDIII at the secondary structure level. Furthermore, we report the ability of chondroitin sulphate C to bind EDIII and induce higher-order dynamic molecular changes at the tertiary and quaternary structure levels which are dependent on pH, GAG species, and the GAG sulphation state. Lastly, we conducted ab initio modelling of Small Angle Neutron Scattering (SANS) data to visualise the induced oligomeric state of EDIII caused by interaction with chondroitin sulphate C, which may aid in TBV development.
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Affiliation(s)
- James G. Hyatt
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (J.G.H.); (C.J.M.-W.); (M.A.S.)
| | - Sylvain Prévost
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble CEDEX 9, France;
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble CEDEX 9, France;
| | - Courtney J. Mycroft-West
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (J.G.H.); (C.J.M.-W.); (M.A.S.)
| | - Mark A. Skidmore
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (J.G.H.); (C.J.M.-W.); (M.A.S.)
| | - Anja Winter
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (J.G.H.); (C.J.M.-W.); (M.A.S.)
- Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble CEDEX 9, France;
- Correspondence: ; Tel.: +44-01782-7-33117
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519
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Morewood R, Nitsche C. A biocompatible stapling reaction for in situ generation of constrained peptides. Chem Sci 2020; 12:669-674. [PMID: 34163798 PMCID: PMC8178976 DOI: 10.1039/d0sc05125j] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Constrained peptides are promising next-generation therapeutics. Peptide stapling is a particularly attractive technique to generate constrained macrocycles with improved biological activity and metabolic stability. We introduce a biocompatible two-component stapling approach based on the reagent 2,6-dicyanopyridine and a pseudo-cysteine amino acid. Stapling can proceed either directly on-resin during solid-phase synthesis or following isolation of the linear peptide. The stapling reaction is orthogonal to natural amino acid side chains and completes in aqueous solution at physiological pH, enabling its direct use in biochemical assays. We performed a small screening campaign of short peptides targeting the Zika virus protease NS2B-NS3, allowing the direct comparison of linear with in situ stapled peptides. A stapled screening hit showed over 28-fold stronger inhibition than its linear analogue, demonstrating the successful identification of constrained peptide inhibitors. A synthetically straightforward and biocompatible peptide-stapling strategy that can be used directly in biochemical assays to identify constrained enzyme inhibitors.![]()
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Affiliation(s)
- Richard Morewood
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
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520
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Pathak S, Parkar H, Tripathi S, Kale A. Ofloxacin as a Disruptor of Actin Aggresome "Hirano Bodies": A Potential Repurposed Drug for the Treatment of Neurodegenerative Diseases. Front Aging Neurosci 2020; 12:591579. [PMID: 33132905 PMCID: PMC7573105 DOI: 10.3389/fnagi.2020.591579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/09/2020] [Indexed: 01/27/2023] Open
Abstract
There is a growing number of aging populations that are more prone to the prevalence of neuropathological disorders. Two major diseases that show a late onset of the symptoms include Alzheimer’s disorder (AD) and Parkinson’s disorder (PD), which are causing an unexpected social and economic impact on the families. A large number of researches in the last decade have focused upon the role of amyloid precursor protein, Aβ-plaque, and intraneuronal neurofibrillary tangles (tau-proteins). However, there is very few understanding of actin-associated paracrystalline structures formed in the hippocampus region of the brain and are called Hirano bodies. These actin-rich inclusion bodies are known to modulate the synaptic plasticity and employ conspicuous effects on long-term potentiation and paired-pulse paradigms. Since the currently known drugs have very little effect in controlling the progression of these diseases, there is a need to develop therapeutic agents, which can have improved efficacy and bioavailability, and can transport across the blood–brain barrier. Moreover, finding novel targets involving compound screening is both laborious and is an expensive process in itself followed by equally tedious Food and Drug Administration (FDA) approval exercise. Finding alternative functions to the already existing FDA-approved molecules for reversing the progression of age-related proteinopathies is of utmost importance. In the current study, we decipher the role of a broad-spectrum general antibiotic (Ofloxacin) on actin polymerization dynamics using various biophysical techniques like right-angle light scattering, dynamic light scattering, circular dichroism spectrometry, isothermal titration calorimetry, scanning electron microscopy, etc. We have also performed in silico docking studies to deduce a plausible mechanism of the drug binding to the actin. We report that actin gets disrupted upon binding to Ofloxacin in a concentration-dependent manner. We have inferred that Ofloxacin, when attached to a drug delivery system, can act as a good candidate for the treatment of neuropathological diseases.
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Affiliation(s)
- Samridhi Pathak
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Haifa Parkar
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Sarita Tripathi
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
| | - Avinash Kale
- School of Chemical Sciences, University of Mumbai - Department of Atomic Energy Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai, India
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521
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Zhu L, Wang L, Matsuura A, Zhang M, Lu P, Iimura K, Nagata K, Suzuki M. Purification, crystallization and X-ray analysis of Pf-SCP (sarcoplasmic Ca-binding protein), related to storage and transport of calcium in mantle of Pinctada fucata. Protein Expr Purif 2020; 178:105781. [PMID: 33137413 DOI: 10.1016/j.pep.2020.105781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/18/2020] [Indexed: 10/23/2022]
Abstract
Pf-SCP, a 21 kDa protein with two EF-hand motifs and a phosphorylation site, was identified from mantle tissue and binds to calcium ions and transports calcium components from cell to the shell of Pinctada fucata. To reveal the molecular basis of the calcium binding activity of Pf-SCP, we expressed the recombinant protein of full-length Pf-SCP in Escherichia coli. Recombinant Pf-SCP (rPf-SCP) purified by Ni affinity chromatography and size exclusion chromatography appeared as a single band on SDS-PAGE. The circular dichroism spectroscopy showed that the α-helix content decreased when rPf-SCP interacted with both calcium ions and calcium carbonate. Western blotting and immunostaining verified the Pf-SCP expression in the shell and localization most in the mantle epithelial cells. To further understand the structural and functional regulation of Pf-SCP by calcium ions and calcium carbonate, the crystallization experiments of rPf-SCP in the presence of calcium ions were performed. A crystal of rPf-SCP obtained in the presence of calcium ions diffracted X-rays up to a resolution of 1.8 Å. The space group of the crystal is C2 with unit cell parameters of a = 96.828 Å, b = 55.906 Å, c = 102.14 Å and β = 90.009°, indicating that three molecules of rPf-SCP are contained in an asymmetric unit as estimated at the value of the Matthews coefficient. These results suggest that Pf-SCP may play a role in calcium ions transportation and shell mineralization by concentrating calcium ions inside the mantle epithelial cells and interacting with calcium carbonate molecules.
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Affiliation(s)
- Lingxiao Zhu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Liying Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akihiro Matsuura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mimin Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Peng Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kurin Iimura
- Food Department, Department of Home Economics, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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522
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Katayama H, Nagata K. Application of 2,2'-dipyridyl disulfide-mediated thiazolidine ring-opening reaction to glycoprotein synthesis: Total chemical synthesis of evasin-3. J Pept Sci 2020; 27:e3290. [PMID: 33118239 DOI: 10.1002/psc.3290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 11/07/2022]
Abstract
Thiazolidine ring-opening reaction is one of the key steps in protein chemical synthesis via sequential native chemical ligation strategy. We recently developed a novel thiazolidine ring-opening reaction with 2,2'-dipyridyl disulfide (DPDS). In order to investigate the applicability of this reaction to glycoprotein synthesis, we synthesized evasin-3, a cysteine-rich glycoprotein with chemokine-binding ability originally found in tick saliva. The sequence of evasin-3 was divided into three segments, and these segments were separately synthesized with the ordinary solid-phase peptide synthesis method. After the first ligation of middle and C-terminal segments, thiazolidine used as a protecting group of Cys residue at the N-terminus of the middle segment was converted to Cys with DPDS. In this thiazolidine ring-opening reaction, DPDS treatment did not affect the N-linked glycan moiety. After the second ligation with the N-terminal segment and the refolding reaction, evasin-3 could be obtained in good yield. The synthetic evasin-3 showed the binding ability specifically to CXCL chemokines. These results clearly indicate that this DPDS method is useful for glycoprotein synthesis.
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Affiliation(s)
- Hidekazu Katayama
- Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Japan
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523
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Bunnak W, Winter AJ, Lazarus CM, Crump MP, Race PR, Wattana-Amorn P. SAXS reveals highly flexible interdomain linkers of tandem acyl carrier protein-thioesterase domains from a fungal nonreducing polyketide synthase. FEBS Lett 2020; 595:133-144. [PMID: 33043457 DOI: 10.1002/1873-3468.13954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 11/07/2022]
Abstract
Menisporopsin A is a fungal bioactive macrocyclic polylactone, the biosynthesis of which requires only reducing (R) and nonreducing (NR) polyketide synthases (PKSs) to guide a series of esterification and cyclolactonization reactions. There is no structural information pertaining to these PKSs. Here, we report the solution characterization of singlet and doublet acyl carrier protein (ACP2 and ACP1 -ACP2 )-thioesterase (TE) domains from NR-PKS involved in menisporopsin A biosynthesis. Small-angle X-ray scattering (SAXS) studies in combination with homology modelling reveal that these polypeptides adopt a distinctive beads-on-a-string configuration, characterized by the presence of highly flexible interdomain linkers. These models provide a platform for studying domain organization and interdomain interactions in fungal NR-PKSs, which may be of value in directing the design of functionally optimized polyketide scaffolds.
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Affiliation(s)
- Waraporn Bunnak
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance, Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | | | | | - Paul R Race
- School of Biochemistry, University of Bristol, UK.,BrisSynBio Synthetic Biology Research Centre, University of Bristol, UK
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance, Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
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524
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Oyeleye AO, Mohd Yusoff SF, Abd Rahim IN, Leow ATC, Saidi NB, Normi YM. Effective refolding of a cysteine rich glycoside hydrolase family 19 recombinant chitinase from Streptomyces griseus by reverse dilution and affinity chromatography. PLoS One 2020; 15:e0241074. [PMID: 33091044 PMCID: PMC7580917 DOI: 10.1371/journal.pone.0241074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
Conventional refolding methods are associated with low yields due to misfolding and high aggregation rates or very dilute proteins. In this study, we describe the optimization of the conventional methods of reverse dilution and affinity chromatography for obtaining high yields of a cysteine rich recombinant glycoside hydrolase family 19 chitinase from Streptomyces griseus HUT6037 (SgChiC). SgChiC is a potential biocontrol agent and a reference enzyme in the study and development of chitinases for various applications. The overexpression of SgChiC was previously achieved by periplasmic localization from where it was extracted by osmotic shock and then purified by hydroxyapatite column chromatography. In the present study, the successful refolding and recovery of recombinant SgChiC (r-SgChiC) from inclusion bodies (IB) by reverse dilution and column chromatography methods is respectively described. Approximately 8 mg of r-SgChiC was obtained from each method with specific activities of 28 and 52 U/mg respectively. These yields are comparable to that obtained from a 1 L culture volume of the same protein isolated from the periplasmic space of E. coli BL21 (DE3) as described in previous studies. The higher yields obtained are attributed to the successful suppression of aggregation by a stepwise reduction of denaturant from high, to intermediate, and finally to low concentrations. These methods are straight forward, requiring the use of fewer refolding agents compared with previously described refolding methods. They can be applied to the refolding of other cysteine rich proteins expressed as inclusion bodies to obtain high yields of actively folded proteins. This is the first report on the recovery of actively folded SgChiC from inclusion bodies.
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Affiliation(s)
- Ayokunmi Omolola Oyeleye
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Siti Faridah Mohd Yusoff
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Izzah Nadiah Abd Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Noor Baity Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M. Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- * E-mail:
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525
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Mao S, Song Z, Wu M, Wang X, Lu F, Qin HM. Expression, Purification, Refolding, and Characterization of a Neverland Protein From Caenorhabditis elegans. Front Bioeng Biotechnol 2020; 8:593041. [PMID: 33195160 PMCID: PMC7609953 DOI: 10.3389/fbioe.2020.593041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/24/2020] [Indexed: 11/23/2022] Open
Abstract
Steroid hormones that serve as vital compounds are necessary for the development and metabolism of a variety of organisms. The neverland (NVD) family genes encode the conserved Rieske-type oxygenases, which are accountable for the dehydrogenation during the synthesis and regulation of steroid hormones. However, the His-tagged NVD protein from Caenorhabditis elegans expresses as inclusion bodies in Escherichia coli BL21 (DE3). This bottleneck can be solved through refolding by urea or the introduction of a maltose-binding protein (MBP) tag at the N-terminus. Through further research on purification after the introduction of a MBP tag at the N-terminus, the CD measurement and fluorescence-based thermal shift assay indicated that MBP was favorable for the NVD proteins' solubility and stability, which may be beneficial for the large-scale manufacture of NVD protein for further research. The structural model contained the Rieske [2Fe-2S] domain and non-heme iron-binding motif, which were similar to 3-ketosteroid 9 α-hydroxylase.
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Affiliation(s)
- Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
| | - Zhan Song
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Mian Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaorui Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
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526
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Wilder LM, Handali PR, Webb LJ, Crooks RM. Interactions between Oligoethylene Glycol-Capped AuNPs and Attached Peptides Control Peptide Structure. Bioconjug Chem 2020; 31:2383-2391. [PMID: 32970412 DOI: 10.1021/acs.bioconjchem.0c00447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide-functionalized nanoparticles (NPs) often rely on a well-defined peptide structure to function. Here, we report the attachment of model peptides to the ligand shell of AuNPs passivated with oligoethylene glycol (OEG). Specifically, peptides containing the repeating (LLKK)n motif plus either one or two reactive functional groups were covalently linked to OEG-capped, ∼5 nm AuNPs via the Cu+-catalyzed azide-alkyne cycloaddition reaction. This work builds on a previous study from our group in which an (LLKK)n peptide having two reactive functional groups was considered. Peptide attachment was confirmed by FTIR spectroscopy. Amino acid analysis was used to determine that 3-4 peptides were immobilized per AuNP. Circular dichroism spectroscopy revealed a structural change from random coil in solution to α-helical upon attachment to OEG-capped AuNPs. The key result of this study is that the nature of the capping layer on the AuNP surface influences peptide structure to a significant degree. Other important findings resulting from this work are that the AuNP-peptide conjugates reported here are water soluble and that the long axis of the helical peptides is oriented tangent to the AuNP surface. The latter point is important for applications involving biorecognition.
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Affiliation(s)
- Logan M Wilder
- Department of Chemistry and Texas Materials Institute, The University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Paul R Handali
- Department of Chemistry and Texas Materials Institute, The University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Lauren J Webb
- Department of Chemistry and Texas Materials Institute, The University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Richard M Crooks
- Department of Chemistry and Texas Materials Institute, The University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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527
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Townsend D, Fullwood NJ, Yates EA, Middleton DA. Aggregation Kinetics and Filament Structure of a Tau Fragment Are Influenced by the Sulfation Pattern of the Cofactor Heparin. Biochemistry 2020; 59:4003-4014. [PMID: 32954725 PMCID: PMC7584336 DOI: 10.1021/acs.biochem.0c00443] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/11/2020] [Indexed: 01/16/2023]
Abstract
A pathological signature of Alzheimer's disease (AD) is the formation of neurofibrillary tangles comprising filamentous aggregates of the microtubule associated protein tau. Tau self-assembly is accelerated by polyanions including heparin, an analogue of heparan sulfate. Tau filaments colocalize with heparan sulfate proteoglycans (HSPGs) in vivo, and HSPGs may also assist the transcellular propagation of tau aggregates. Here, we investigate the role of the sulfate moieties of heparin in the aggregation of a recombinant tau fragment Δtau187, comprising residues 255-441 of the C-terminal microtubule-binding domain. The effects that the selective removal of the N-, 2-O-, and 6-O-sulfate groups from heparin have on the kinetics of tau aggregation, aggregate morphology, and protein structure and dynamics were examined. Aggregation kinetics monitored by thioflavin T (ThT) fluorescence revealed that aggregation is considerably slower in the presence of 2-O-desulfated heparin than with N- or 6-O-desulfated heparin. Transmission electron microscopy revealed that tau filaments induced by 2-O-desulfated heparin were more slender than filaments formed in the presence of intact heparin or 6-O-desulfated heparin. The 2-O-desulfated heparin-induced filaments had more extensive regions of flexibility than the other filaments, according to circular dichroism and solid-state NMR spectroscopy. These results indicate that the sulfation pattern of heparin regulates tau aggregation, not purely though electrostatic forces but also through conformational perturbations of heparin when the 2-O-sulfate is removed. These findings may have implications for the progression of AD, as the sulfation pattern of GAGs is known to change during the aging process, which is the main risk factor for the disease.
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Affiliation(s)
- David Townsend
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, U.K.
| | - Nigel J. Fullwood
- Division
of Biomedical and Life Sciences, University
of Lancaster, Lancaster LA1 4YG, U.K.
| | - Edwin A. Yates
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - David A. Middleton
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, U.K.
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528
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Páez-Pérez E, Llamas-García ML, Benítez-Cardoza CG, Montero-Morán GM, Lara-González S. Bioinformatic Analysis and Biophysical Characterization Reveal Structural Disorder in G0S2 Protein. ACS OMEGA 2020; 5:25841-25847. [PMID: 33073109 PMCID: PMC7557935 DOI: 10.1021/acsomega.0c03171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
G0S2 is a small protein of 103 residues in length that is involved in multiple cellular processes. To date, several reports have shown that G0S2 functions by making direct protein-protein interactions with key proteins. In lipolysis, G0S2 specifically interacts with adipose triglyceride lipase, inhibiting its activity and resulting in lipolysis being downregulated. In a similar way, G0S2 also participates in the regulation of apoptosis, cell proliferation, and oxidative phosphorylation; however, information regarding G0S2 structural and biophysical properties is limited. In this work, we conducted a comparative structural analysis of human and mouse G0S2 proteins. Bioinformatics suggests the presence of a disordered C-terminal region in human G0S2. Experimental characterization by size-exclusion chromatography and dynamic light scattering showed that human and mouse G0S2 have different hydrodynamic properties. In comparison to the mouse G0S2, which behaves similar to a globular protein, the human G0S2 shows an elongated conformation, most likely by displaying a disordered C-terminal region. Further analysis of hydrodynamic properties under denaturing conditions suggests the presence of a structural element in the mouse protein that undergoes an order to disorder transition at low urea concentration. Structural analysis by circular dichroism revealed that in native conditions, both proteins are mainly unstructured, showing the presence of beta sheet structures. Further analysis of CD data suggests that both proteins belong to the premolten globule family of intrinsically disordered proteins. We suggest that the intrinsic disorder observed in the G0S2 protein may facilitate its interaction with multiple partners in the regulation of cellular metabolism.
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Affiliation(s)
- Edgar
D. Páez-Pérez
- IPICYT,
División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica
A. C., San Luis Potosí 78216, México
| | - Miriam Livier Llamas-García
- IPICYT,
División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica
A. C., San Luis Potosí 78216, México
| | - Claudia G. Benítez-Cardoza
- Laboratorio
de Investigación Bioquímica, Programa Institucional
en Biomedicina Molecular ENMyH-Instituto Politécnico Nacional, Ciudad de México 07320, México
| | - Gabriela M. Montero-Morán
- Facultad
de Ciencias Químicas, Laboratorio IBCM, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, México
| | - Samuel Lara-González
- IPICYT,
División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica
A. C., San Luis Potosí 78216, México
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529
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Abstract
Ethanol is a chemoattractant for Bacillus subtilis even though it is not metabolized and inhibits growth. B. subtilis likely uses ethanol to find ethanol-fermenting microorganisms to utilize as prey. Two chemoreceptors sense ethanol: HemAT and McpB. HemAT’s myoglobin-like sensing domain directly binds ethanol, but the heme group is not involved. McpB is a transmembrane receptor consisting of an extracellular sensing domain and a cytoplasmic signaling domain. While most attractants bind the extracellular sensing domain, we found that ethanol directly binds between intermonomer helices of the cytoplasmic signaling domain of McpB, using a mechanism akin to those identified in many mammalian ethanol-binding proteins. Our results indicate that the sensory repertoire of chemoreceptors extends beyond the sensing domain and can directly involve the signaling domain. Motile bacteria sense chemical gradients using chemoreceptors, which consist of distinct sensing and signaling domains. The general model is that the sensing domain binds the chemical and the signaling domain induces the tactic response. Here, we investigated the unconventional sensing mechanism for ethanol taxis in Bacillus subtilis. Ethanol and other short-chain alcohols are attractants for B. subtilis. Two chemoreceptors, McpB and HemAT, sense these alcohols. In the case of McpB, the signaling domain directly binds ethanol. We were further able to identify a single amino acid residue, Ala431, on the cytoplasmic signaling domain of McpB that, when mutated to serine, reduces taxis to alcohols. Molecular dynamics simulations suggest that the conversion of Ala431 to serine increases coiled-coil packing within the signaling domain, thereby reducing the ability of ethanol to bind between the helices of the signaling domain. In the case of HemAT, the myoglobin-like sensing domain binds ethanol, likely between the helices encapsulating the heme group. Aside from being sensed by an unconventional mechanism, ethanol also differs from many other chemoattractants because it is not metabolized by B. subtilis and is toxic. We propose that B. subtilis uses ethanol and other short-chain alcohols to locate prey, namely, alcohol-producing microorganisms.
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530
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A Calcium Sensor Discovered in Bluetongue Virus Nonstructural Protein 2 Is Critical for Virus Replication. J Virol 2020; 94:JVI.01099-20. [PMID: 32759321 PMCID: PMC7527055 DOI: 10.1128/jvi.01099-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
After entering the host cells, viruses use cellular host factors to ensure a successful virus replication process. For replication in infected cells, members of the Reoviridae family form inclusion body-like structures known as viral inclusion bodies (VIB) or viral factories. Bluetongue virus (BTV) forms VIBs in infected cells through nonstructural protein 2 (NS2), a phosphoprotein. An important regulatory factor critical for VIB formation is phosphorylation of NS2. In our study, we discovered a characteristic calcium-binding EF-hand-like motif in NS2 and found that the calcium binding preferentially affects phosphorylation level of the NS2 and has a role in regulating VIB assembly. Many viruses use specific viral proteins to bind calcium ions (Ca2+) for stability or to modify host cell pathways; however, to date, no Ca2+ binding protein has been reported in bluetongue virus (BTV), the causative agent of bluetongue disease in livestock. Here, using a comprehensive bioinformatics screening, we identified a putative EF-hand-like Ca2+ binding motif in the carboxyl terminal region of BTV nonstructural phosphoprotein 2 (NS2). Subsequently, using a recombinant NS2, we demonstrated that NS2 binds Ca2+ efficiently and that Ca2+ binding was perturbed when the Asp and Glu residues in the motif were substituted by alanine. Using circular dichroism analysis, we found that Ca2+ binding by NS2 triggered a helix-to-coil secondary structure transition. Further, cryo-electron microscopy in the presence of Ca2+ revealed that NS2 forms helical oligomers which, when aligned with the N-terminal domain crystal structure, suggest an N-terminal domain that wraps around the C-terminal domain in the oligomer. Further, an in vitro kinase assay demonstrated that Ca2+ enhanced the phosphorylation of NS2 significantly. Importantly, mutations introduced at the Ca2+ binding site in the viral genome by reverse genetics failed to allow recovery of viable virus, and the NS2 phosphorylation level and assembly of viral inclusion bodies (VIBs) were reduced. Together, our data suggest that NS2 is a dedicated Ca2+ binding protein and that calcium sensing acts as a trigger for VIB assembly, which in turn facilitates virus replication and assembly. IMPORTANCE After entering the host cells, viruses use cellular host factors to ensure a successful virus replication process. For replication in infected cells, members of the Reoviridae family form inclusion body-like structures known as viral inclusion bodies (VIB) or viral factories. Bluetongue virus (BTV) forms VIBs in infected cells through nonstructural protein 2 (NS2), a phosphoprotein. An important regulatory factor critical for VIB formation is phosphorylation of NS2. In our study, we discovered a characteristic calcium-binding EF-hand-like motif in NS2 and found that the calcium binding preferentially affects phosphorylation level of the NS2 and has a role in regulating VIB assembly.
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531
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Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs. Mol Cell 2020; 80:227-236.e5. [PMID: 32991829 DOI: 10.1016/j.molcel.2020.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/16/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.
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532
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Grafskaia E, Pavlova E, Babenko VV, Latsis I, Malakhova M, Lavrenova V, Bashkirov P, Belousov D, Klinov D, Lazarev V. The Hirudo Medicinalis Microbiome Is a Source of New Antimicrobial Peptides. Int J Mol Sci 2020; 21:E7141. [PMID: 32992666 PMCID: PMC7582656 DOI: 10.3390/ijms21197141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/23/2022] Open
Abstract
Antimicrobial peptides (AMPs) are considered a promising new class of anti-infectious agents. This study reports new antimicrobial peptides derived from the Hirudo medicinalis microbiome identified by a computational analysis method applied to the H. medicinalis metagenome. The identified AMPs possess a strong antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC range: 5.3 to 22.4 μM), including Staphylococcus haemolyticus, an opportunistic coagulase-negative pathogen. The secondary structure analysis of peptides via CD spectroscopy showed that all the AMPs except pept_352 have mostly disordered structures that do not change under different conditions. For peptide pept_352, the α-helical content increases in the membrane environment. The examination of the mechanism of action of peptides suggests that peptide pept_352 exhibits a direct membranolytic activity. Furthermore, the cytotoxicity assay demonstrated that the nontoxic peptide pept_1545 is a promising candidate for drug development. Overall, the analysis method implemented in the study may serve as an effective tool for the identification of new AMPs.
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Affiliation(s)
- Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Elizaveta Pavlova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow 141701, Russia
| | - Vladislav V. Babenko
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Ivan Latsis
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Maja Malakhova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Victoria Lavrenova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
- Department of biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Pavel Bashkirov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Dmitrii Belousov
- Sechenov First Moscow State Medical University Sechenov University, Moscow 119991, Russia;
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (E.P.); (V.V.B.); (I.L.); (M.M.); (V.L.); (P.B.); (D.K.)
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow 141701, Russia
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533
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Wolska A, Lo L, Sviridov DO, Pourmousa M, Pryor M, Ghosh SS, Kakkar R, Davidson M, Wilson S, Pastor RW, Goldberg IJ, Basu D, Drake SK, Cougnoux A, Wu MJ, Neher SB, Freeman LA, Tang J, Amar M, Devalaraja M, Remaley AT. A dual apolipoprotein C-II mimetic-apolipoprotein C-III antagonist peptide lowers plasma triglycerides. Sci Transl Med 2020; 12:12/528/eaaw7905. [PMID: 31996466 DOI: 10.1126/scitranslmed.aaw7905] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022]
Abstract
Recent genetic studies have established that hypertriglyceridemia (HTG) is causally related to cardiovascular disease, making it an active area for drug development. We describe a strategy for lowering triglycerides (TGs) with an apolipoprotein C-II (apoC-II) mimetic peptide called D6PV that activates lipoprotein lipase (LPL), the main plasma TG-hydrolyzing enzyme, and antagonizes the TG-raising effect of apoC-III. The design of D6PV was motivated by a combination of all-atom molecular dynamics simulation of apoC-II on the Anton 2 supercomputer, structural prediction programs, and biophysical techniques. Efficacy of D6PV was assessed ex vivo in human HTG plasma and was found to be more potent than full-length apoC-II in activating LPL. D6PV markedly lowered TG by more than 80% within a few hours in both apoC-II-deficient mice and hAPOC3-transgenic (Tg) mice. In hAPOC3-Tg mice, D6PV treatment reduced plasma apoC-III by 80% and apoB by 65%. Furthermore, low-density lipoprotein (LDL) cholesterol did not accumulate but rather was decreased by 10% when hAPOC3-Tg mice lacking the LDL-receptor (hAPOC3-Tg × Ldlr-/- ) were treated with the peptide. D6PV lowered TG by 50% in whole-body inducible Lpl knockout (iLpl-/- ) mice, confirming that it can also act independently of LPL. D6PV displayed good subcutaneous bioavailability of about 80% in nonhuman primates. Because it binds to high-density lipoproteins, which serve as a long-term reservoir, it also has an extended terminal half-life (42 to 50 hours) in nonhuman primates. In summary, D6PV decreases plasma TG by acting as a dual apoC-II mimetic and apoC-III antagonist, thereby demonstrating its potential as a treatment for HTG.
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Affiliation(s)
- Anna Wolska
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Larry Lo
- Corvidia Therapeutics Inc., Waltham, MA 02451, USA
| | - Denis O Sviridov
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohsen Pourmousa
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Milton Pryor
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Rahul Kakkar
- Corvidia Therapeutics Inc., Waltham, MA 02451, USA
| | | | - Sierra Wilson
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira J Goldberg
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Debapriya Basu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Antony Cougnoux
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Jing Wu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Saskia B Neher
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lita A Freeman
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jingrong Tang
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcelo Amar
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Alan T Remaley
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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534
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Nakamura S, Kibria MG, Unzai S, Kuroda Y, Kidokoro SI. Reversible Oligomerization and Reverse Hydrophobic Effect Induced by Isoleucine Tags Attached at the C-Terminus of a Simplified BPTI Variant. Biochemistry 2020; 59:3660-3668. [PMID: 32924442 DOI: 10.1021/acs.biochem.0c00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein amorphous aggregation has become the focus of great attention, as it can impair the ability of cells to function properly. Here, we evaluated the effects of three peptide tags, consisting of one, three, and five consecutive isoleucines attached at the C-terminus end of a simplified bovine pancreatic trypsin inhibitor (BPTI) variant, BPTI-19A, on the thermal stability and oligomerization by circular dichroism spectrometry and differential scanning calorimetry in detail. All of the BPTI-19A variants exhibited a reversible and apparently two-state thermal transition like BPTI-19A at pH 4.7. The thermal transition of the five-isoleucine-tagged variant showed clear protein-concentration dependence, where the apparent denaturation temperature decreased as the protein concentration increased. Quantitative analysis indicated that this phenomenon originated from the presence of reversibly oligomerized (RO) states at high temperatures. The results also illustrated that the thermodynamic stability difference between the native and the monomeric denatured state in all the proteins was destabilized by the hydrophobic tags and was well explained by the reverse hydrophobic effect due to the tags. The existence of the RO states was confirmed by both analytical ultracentrifugation and dynamic light scattering. This indicated that the five-isoleucine hydrophobic tag is strong enough to induce intermolecular hydrophobic contact among the denatured molecules leading to oligomerization, and even one- or three-isoleucine tags are effective enough to generate intramolecular hydrophobic contact, thus provoking denaturation through the reverse hydrophobic effect.
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Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of General Education, National Institute of Technology, Ube College, 2-14-1 Tokiwadai, Ube, Yamaguchi 755-8555, Japan
| | - Md Golam Kibria
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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535
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Assafa TE, Nandi S, Śmiłowicz D, Galazzo L, Teucher M, Elsner C, Pütz S, Bleicken S, Robin AY, Westphal D, Uson I, Stoll R, Czabotar PE, Metzler-Nolte N, Bordignon E. Biophysical Characterization of Pro-apoptotic BimBH3 Peptides Reveals an Unexpected Capacity for Self-Association. Structure 2020; 29:114-124.e3. [PMID: 32966763 DOI: 10.1016/j.str.2020.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/13/2020] [Accepted: 08/29/2020] [Indexed: 01/11/2023]
Abstract
Bcl-2 proteins orchestrate the mitochondrial pathway of apoptosis, pivotal for cell death. Yet, the structural details of the conformational changes of pro- and antiapoptotic proteins and their interactions remain unclear. Pulse dipolar spectroscopy (double electron-electron resonance [DEER], also known as PELDOR) in combination with spin-labeled apoptotic Bcl-2 proteins unveils conformational changes and interactions of each protein player via detection of intra- and inter-protein distances. Here, we present the synthesis and characterization of pro-apoptotic BimBH3 peptides of different lengths carrying cysteines for labeling with nitroxide or gadolinium spin probes. We show by DEER that the length of the peptides modulates their homo-interactions in the absence of other Bcl-2 proteins and solve by X-ray crystallography the structure of a BimBH3 tetramer, revealing the molecular details of the inter-peptide interactions. Finally, we prove that using orthogonal labels and three-channel DEER we can disentangle the Bim-Bim, Bcl-xL-Bcl-xL, and Bim-Bcl-xL interactions in a simplified interactome.
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Affiliation(s)
- Tufa E Assafa
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sukhendu Nandi
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Dariusz Śmiłowicz
- Chair of Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Christina Elsner
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefanie Pütz
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stephanie Bleicken
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Adeline Y Robin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Dana Westphal
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia; Department of Dermatology, Medical Faculty and University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Isabel Uson
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain; ICREA, Baldiri Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Nils Metzler-Nolte
- Chair of Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
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536
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Agrillo B, Proroga YTR, Gogliettino M, Balestrieri M, Tatè R, Nicolais L, Palmieri G. A Safe and Multitasking Antimicrobial Decapeptide: The Road from De Novo Design to Structural and Functional Characterization. Int J Mol Sci 2020; 21:E6952. [PMID: 32971824 PMCID: PMC7555028 DOI: 10.3390/ijms21186952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial peptides (AMPs) are excellent candidates to fight multi-resistant pathogens worldwide and are considered promising bio-preservatives to control microbial spoilage through food processing. To date, designing de novo AMPs with high therapeutic indexes, low-cost synthesis, high resistance, and bioavailability, remains a challenge. In this study, a novel decapeptide, named RiLK1, was rationally designed starting from the sequence of the previously characterized AMP 1018-K6, with the aim of developing short peptides, and promoting higher selectivity over mammalian cells, antibacterial activity, and structural resistance under different salt, pH, and temperature conditions. Interestingly, RiLK1 displayed a broad-spectrum of bactericidal activity against Gram-positive and Gram-negative bacteria, including multidrug resistant clinical isolates of Salmonella species, with Minimal Bactericidal Concentration (MBC) values in low micromolar range, and it was effective even against two fungal pathogens with no evidence of cytotoxicity on human keratinocytes and fibroblasts. Moreover, RiLK1-activated polypropylene films were revealed to efficiently prevent the growth of microbial spoilage, possibly improving the shelf life of fresh food products. These results suggested that de novo designed peptide RiLK1 could be the first candidate for the development of a promising class of decameric and multitask antimicrobial agents to overcome drug-resistance phenomena.
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Affiliation(s)
| | - Yolande T. R. Proroga
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Marta Gogliettino
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), 80131 Napoli, Italy; (M.G.); (M.B.)
| | - Marco Balestrieri
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), 80131 Napoli, Italy; (M.G.); (M.B.)
| | - Rosarita Tatè
- Institute of Genetics and Biophysics, National Research Council (IGB-CNR), 80131 Naples, Italy;
| | | | - Gianna Palmieri
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), 80131 Napoli, Italy; (M.G.); (M.B.)
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537
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New Factors Enhancing the Reactivity of Cysteines in Molten Globule-Like Structures. Int J Mol Sci 2020; 21:ijms21186949. [PMID: 32971812 PMCID: PMC7555924 DOI: 10.3390/ijms21186949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 01/10/2023] Open
Abstract
Protein cysteines often play crucial functional and structural roles, so they are emerging targets to design covalent thiol ligands that are able to modulate enzyme or protein functions. Some of these residues, especially those involved in enzyme mechanisms—including nucleophilic and reductive catalysis and thiol-disulfide exchange—display unusual hyper-reactivity; such a property is expected to result from a low pKa and from a great accessibility to a given reagent. New findings and previous evidence clearly indicate that pKa perturbations can only produce two–four-times increased reactivity at physiological pH values, far from the hundred and even thousand-times kinetic enhancements observed for some protein cysteines. The data from the molten globule-like structures of ribonuclease, lysozyme, bovine serum albumin and chymotrypsinogen identified new speeding agents, i.e., hydrophobic/electrostatic interactions and productive complex formations involving the protein and thiol reagent, which were able to confer exceptional reactivity to structural cysteines which were only intended to form disulfides. This study, for the first time, evaluates quantitatively the different contributions of pKa and other factors to the overall reactivity. These findings may help to clarify the mechanisms that allow a rapid disulfide formation during the oxidative folding of many proteins.
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538
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Johnson SN, Griffin JD, Hulbert C, DeKosky BJ, Thomas JW, Berkland CJ. Multimeric Insulin Desensitizes Insulin-Specific B Cells. ACS APPLIED BIO MATERIALS 2020; 3:6319-6330. [DOI: 10.1021/acsabm.0c00782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Stephanie N. Johnson
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - J. Daniel Griffin
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
| | - Chrys Hulbert
- Department of Medicine, Division of Rheumatology, and Immunology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045, United States
| | - James W. Thomas
- Department of Medicine, Division of Rheumatology, and Immunology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Cory J. Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045, United States
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539
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Olmos J, Pignataro MF, Benítez dos Santos AB, Bringas M, Klinke S, Kamenetzky L, Velazquez F, Santos J. A Highly Conserved Iron-Sulfur Cluster Assembly Machinery between Humans and Amoeba Dictyostelium discoideum: The Characterization of Frataxin. Int J Mol Sci 2020; 21:E6821. [PMID: 32957566 PMCID: PMC7554988 DOI: 10.3390/ijms21186821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Several biological activities depend on iron-sulfur clusters ([Fe-S]). Even though they are well-known in several organisms their function and metabolic pathway were poorly understood in the majority of the organisms. We propose to use the amoeba Dictyostelium discoideum, as a biological model to study the biosynthesis of [Fe-S] at the molecular, cellular and organism levels. First, we have explored the D. discoideum genome looking for genes corresponding to the subunits that constitute the molecular machinery for Fe-S cluster assembly and, based on the structure of the mammalian supercomplex and amino acid conservation profiles, we inferred the full functionality of the amoeba machinery. After that, we expressed the recombinant mature form of D. discoideum frataxin protein (DdFXN), the kinetic activator of this pathway. We characterized the protein and its conformational stability. DdFXN is monomeric and compact. The analysis of the secondary structure content, calculated using the far-UV CD spectra, was compatible with the data expected for the FXN fold, and near-UV CD spectra were compatible with the data corresponding to a folded protein. In addition, Tryptophan fluorescence indicated that the emission occurs from an apolar environment. However, the conformation of DdFXN is significantly less stable than that of the human FXN, (4.0 vs. 9.0 kcal mol-1, respectively). Based on a sequence analysis and structural models of DdFXN, we investigated key residues involved in the interaction of DdFXN with the supercomplex and the effect of point mutations on the energetics of the DdFXN tertiary structure. More than 10 residues involved in Friedreich's Ataxia are conserved between the human and DdFXN forms, and a good correlation between mutational effect on the energetics of both proteins were found, suggesting the existence of similar sequence/function/stability relationships. Finally, we integrated this information in an evolutionary context which highlights particular variation patterns between amoeba and humans that may reflect a functional importance of specific protein positions. Moreover, the complete pathway obtained forms a piece of evidence in favor of the hypothesis of a shared and highly conserved [Fe-S] assembly machinery between Human and D. discoideum.
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Affiliation(s)
- Justo Olmos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - María Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Ana Belén Benítez dos Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Buenos Aires C1428EGA, Argentina;
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina;
| | - Laura Kamenetzky
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Francisco Velazquez
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)—(UBA/CONICET), Buenos Aires C1428EGA, Argentina
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, Buenos Aires C1033AAJ, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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540
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Jaramillo-Ramírez J, Marcial-Bazaldua N, Sánchez-Puig N. Characterisation of the interaction of guanine nucleotides with ribosomal GTPase Lsg1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140538. [PMID: 32916301 DOI: 10.1016/j.bbapap.2020.140538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 08/06/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Ribosome biogenesis in eukaryotes requires the participation of several transactivation factors that are involved in the modification, assembly, transport and quality control of the ribosomal subunits. One of these factors is the Large subunit GTPase 1 (Lsg1), a protein that acts as the release factor for the export adaptor named Nonsense-mediated mRNA decay 3 protein (Nmd3) and facilitates the incorporation of the last structural protein uL16 into the 60S subunit. Here, we characterised the recombinant yeast Lsg1 and studied its catalysis and binding properties for guanine nucleotides. We described the interaction of Lsg1 with guanine nucleotides alone and in the presence of the complex Nmd3•60S using fluorescence spectroscopy. Lsg1 has a greater affinity for GTP than for GDP suggesting that in the cell cytoplasm it exists mainly bound to the former. In the presence of 60S subunits loaded with Nmd3, the affinity of Lsg1 for both nucleotides increases but to a larger extent towards GTP. From this observation together with the excess of GTP present in the cytoplasm of exponentially growing cells over that of GDP, we can infer that the pre-ribosomal particle composed by Nmd3•60S acts as a GTP Stabilising Factor for Lsg1. Additionally, Lsg1 undergoes different conformational changes depending on its binding partner or the guanine nucleotides it interacts with. Steady-state kinetic analysis of free Lsg1 indicated slow GTP hydrolysis with values of kcat 1 min-1 and Km of 34 μM.
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Affiliation(s)
- Juliana Jaramillo-Ramírez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Nancy Marcial-Bazaldua
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Nuria Sánchez-Puig
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico..
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541
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Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation. mBio 2020; 11:mBio.02052-20. [PMID: 32900808 PMCID: PMC7482068 DOI: 10.1128/mbio.02052-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development. This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.
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542
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Acosta S, Poocza L, Quintanilla-Sierra L, Rodríguez-Cabello JC. Charge Density as a Molecular Modulator of Nanostructuration in Intrinsically Disordered Protein Polymers. Biomacromolecules 2020; 22:158-170. [PMID: 32840359 DOI: 10.1021/acs.biomac.0c00934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Intrinsically disordered protein polymers (IDPPs) have attracted a lot of attention in the development of bioengineered devices and for use as study models in molecular biology because of their biomechanical properties and stimuli-responsiveness. The present study aims to understand the effect of charge density on the self-assembly of IDPPs. To that end, a library of recombinant IDPPs based on an amphiphilic diblock design with different charge densities was bioproduced, and their supramolecular assembly was characterized on the nano-, meso-, and microscale. Although the phase transition was driven by the collapse of hydrophobic moieties, the hydrophilic block composition strongly affected hierarchical assembly and, therefore, enabled the production of new molecular architectures, thus leading to new dynamics that govern the liquid-gel transition. These results highlight the importance of electrostatic repulsion for the hierarchical assembly of IDPPs and provide insights into the manufacture of supramolecular protein-based materials.
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Affiliation(s)
- Sergio Acosta
- Bioforge Lab, CIBER-BBN, University of Valladolid, Paseo Belén 19, 47011, Valladolid, Spain
| | - Leander Poocza
- Bioforge Lab, CIBER-BBN, University of Valladolid, Paseo Belén 19, 47011, Valladolid, Spain
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543
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Panchamia B, Raimalani V, Prashar V, Kumar M, Ratna Prabha C. Structural and Functional Characterisation of the Domains of Ubiquitin-Activating Enzyme (E1) of Saccharomyces cerevisiae. Cell Biochem Biophys 2020; 78:309-319. [PMID: 32583128 DOI: 10.1007/s12013-020-00924-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/05/2020] [Indexed: 10/23/2022]
Abstract
Ubiquitin-activating enzyme (E1) is the first enzyme of the ubiquitination pathway and is required to activate ubiquitin. E1 of Saccharomyces cerevisiae is a large multidomain monomeric protein. There are no studies available on the domains of yeast E1 as independent entities. Four domains of E1 namely, first catalytic cysteine half-domain (FCCH), four-helix bundle (4HB), second catalytic cysteine half-domain (SCCH) and ubiquitin fold domain (UFD) were characterised to understand their structural and functional independence vis-a-vis full length E1. Spectroscopic characterisation using circular dichroism and fluorescence suggested that these domains can act as independent folding units and attain native-like secondary structure. The structural features obtained with the peptides SCCH and FCCH of S. cerevisiae bear a high degree of structural similarity to the corresponding fragments of mouse from literature. Nearly 50% of the residues of the 4HB domain of the S. cerevisiae sample showed helical conformation. They displayed a high degree of conservation when compared with 4HB of mouse with respect to their identity and arrangement. The fragment UFD of yeast formed an α/β domain as in the whole protein and exhibited 45% homology with that of mouse, showing a similar arrangement of α and β elements in its secondary structure. Overexpression of the domains in vivo indicated that the SCCH domain and to some extent UFD apparently interfere with cellular functions such as survival under various stresses.
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Affiliation(s)
- Brinda Panchamia
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
| | - Varsha Raimalani
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
| | - Vishal Prashar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 450085, India
| | - Mukesh Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 450085, India
| | - C Ratna Prabha
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India.
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544
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Kaur J, Giri A, Bhattacharya M. The protein-surfactant stoichiometry governs the conformational switching and amyloid nucleation kinetics of tau K18. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2020; 49:425-434. [PMID: 32691116 DOI: 10.1007/s00249-020-01447-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Amyloids are pathological hallmarks of a number of debilitating neurodegenerative diseases. Understanding the molecular mechanism of protein amyloid assembly with an emphasis on structural characterization of early, key prefibrillar species is important for targeted drug design and clinical interventions. Tau is an intrinsically disordered, microtubule-binding protein which is also implicated in various neurodegenerative disorders such as frontotemporal dementia, Down's syndrome, Alzheimer's disease, etc. Earlier reports have demonstrated that tau aggregation in vitro is triggered by anionic inducers, presumably due to charge compensation which facilitates intermolecular association between the tau polypeptide chains. However, the molecular mechanism of tau amyloid aggregation, involving the structural characterization of amyloidogenic intermediates formed especially during early key steps, remains elusive. In this work, we have employed a spectroscopic toolbox to elucidate the mechanism of anionic surfactant-induced disorder-to-order amyloid transition of a tau segment. This study revealed that the amyloid assembly is mediated via binding-induced conformational switching into an early partially helical amyloid-competent intermediate. Additionally, protein and inducer concentration-dependent studies indicated that at the higher protein and/or inducer concentrations, competing off-pathway intermediates dampen the amyloid assembly which implies that the stoichiometry of protein and inducer plays a key regulatory role in the amyloid nucleation and fibril elongation kinetics.
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Affiliation(s)
- Jaspreet Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab, 147004, India
| | - Anjali Giri
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab, 147004, India
| | - Mily Bhattacharya
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab, 147004, India.
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545
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Vane EW, He S, Maibaum L, Nath A. Rapid Formation of Peptide/Lipid Coaggregates by the Amyloidogenic Seminal Peptide PAP 248-286. Biophys J 2020; 119:924-938. [PMID: 32814060 PMCID: PMC7474197 DOI: 10.1016/j.bpj.2020.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/27/2022] Open
Abstract
Protein/lipid coassembly is an understudied phenomenon that is important to the function of antimicrobial peptides as well as the pathological effects of amyloid. Here, we study the coassembly process of PAP248-286, a seminal peptide that displays both amyloid-forming and antimicrobial activity. PAP248-286 is a peptide fragment of prostatic acid phosphatase and has been reported to form amyloid fibrils, known as semen-derived enhancer of viral infection (SEVI), that enhance the viral infectivity of human immunodeficiency virus. We find that in addition to forming amyloid, PAP248-286 much more readily assembles with lipid vesicles into peptide/lipid coaggregates that resemble amyloid fibrils in some important ways but are a distinct species. The formation of these PAP248-286/lipid coaggregates, which we term "messicles," is controlled by the peptide:lipid (P:L) ratio and by the lipid composition. The optimal P:L ratio is around 1:10, and at least 70% anionic lipid is required for coaggregate formation. Once formed, messicles are not disrupted by subsequent changes in P:L ratio. We propose that messicles form through a polyvalent assembly mechanism, in which a critical surface density of PAP248-286 on liposomes enables peptide-mediated particle bridging into larger species. Even at ∼50-fold lower PAP248-286 concentrations, messicles form at least 10-fold faster than amyloid fibrils. It is therefore possible that some or all of the biological activities assigned to SEVI, the amyloid form of PAP248-286, could instead be attributed to a PAP248-286/lipid coaggregate. More broadly speaking, this work could provide a potential framework for the discovery and characterization of nonamyloid peptide/lipid coaggregates by other amyloid-forming proteins and antimicrobial peptides.
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Affiliation(s)
- Eleanor W Vane
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington; Biological Physics, Structure and Design Program, University of Washington, Seattle, Washington
| | - Shushan He
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington; Biological Physics, Structure and Design Program, University of Washington, Seattle, Washington.
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546
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Wu MH, Chan AC, Tu LH. Role of lysine residue of islet amyloid polypeptide in fibril formation, membrane binding, and inhibitor binding. Biochimie 2020; 177:153-163. [PMID: 32860895 DOI: 10.1016/j.biochi.2020.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/31/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022]
Abstract
The aggregation of islet amyloid polypeptide (IAPP) is implicated in the pathogenesis of type 2 diabetes (T2D). In T2D, this peptide aggregates to form amyloid fibrils; the mechanism responsible for islet amyloid formation is unclear. However, it is known that the aggregation propensity of IAPP is highly related to its primary sequence. Several residues have been suggested to be critical in modulating IAPP amyloid formation, but role of the sole lysine residue at position 1 (Lys-1) in IAPP has not been discussed. In our previous study, we found that glycated IAPP can form amyloid faster than normal IAPP and induce normal IAPP to expedite the aggregation process. To gain more insight into the contribution of Lys-1 in the kinetics of fibril formation, we synthesized another two IAPP variants, K1E-IAPP and K1Nle-IAPP, in which the Lys residue was mutated to glutamate and norleucine, respectively. Interestingly, we observed that the negative or neutral charged side chain at this position was preferred for amyloid formation. The findings suggested this residue may take part in the inter- or intra-molecular interaction during IAPP aggregation, even though it was proposed not to be in part of fibril core structure. Our data also revealed that the inhibitory mechanism of some inhibitors for IAPP aggregation require reaction with Lys-1. Modifications of Lys-1, such as protein glycation, may affect the effectiveness of the inhibitory action of some potential drugs in the treatment of amyloidosis.
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Affiliation(s)
- Meng-Hsin Wu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Ai-Ci Chan
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Ling-Hsien Tu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan.
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547
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Sathyaseelan C, Vijayakumar V, Rathinavelan T. CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Kohonen Algorithms. J Mol Biol 2020; 433:166629. [PMID: 32841657 DOI: 10.1016/j.jmb.2020.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Nucleic acids exhibit a repertoire of conformational preference depending on the sequence and environment. Circular dichroism (CD) is an essential and valuable tool for monitoring such secondary structural conformations of nucleic acids. Nonetheless, the CD spectral diversity associated with these structures poses a challenge in obtaining the quantitative information about the secondary structural content of a given CD spectrum. To this end, the competence of the extreme gradient boosting decision-tree (XGBoost), Kohonen and neural network (nnet) algorithms have been exploited here to predict the diverse secondary structures of nucleic acids. A curated library of 450 CD spectra corresponding to 16 different secondary structures of nucleic acids has been created and used as a training dataset. The hyper-parameters corresponding to the aforementioned algorithms have been optimized using holdout and k-fold (here, k = 5) cross-validation methods. For a test dataset of 150 CD spectra, both the nnet and XGBoost algorithms have exhibited nearly similar prediction accuracy in the range of 85% and 87% (the latter exhibited a slightly higher prediction accuracy). Thus, the nnet and XGBoost algorithms tested here can be employed for predicting the hybrid nucleic acid topologies in future. For the sake of accessibility, the entire process has been automated and implemented as a webserver, called CD-NuSS (CD to nucleic acids secondary structure) and is freely accessible at https://project.iith.ac.in/cdnuss/.
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Affiliation(s)
- Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana,502285, India
| | - Vinothini Vijayakumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana,502285, India
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548
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He J, Becares ER, Thulstrup PW, Gamon LF, Pedersen JN, Otzen D, Gourdon P, Davies MJ, Hägglund P. Peroxynitrous acid (ONOOH) modifies the structure of anastellin and influences its capacity to polymerize fibronectin. Redox Biol 2020; 36:101631. [PMID: 32807731 PMCID: PMC7364157 DOI: 10.1016/j.redox.2020.101631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/18/2020] [Accepted: 06/28/2020] [Indexed: 11/27/2022] Open
Abstract
Anastellin (AN), a fragment of the first type III module in fibronectin (FN), initiates formation of superfibronectin, a polymer which resembles the native cell-derived fibrillar FN found in the extracellular matrix of many tissues, but which displays remarkably different functional properties. Here we demonstrate that exposure of AN to the biologically-important inflammatory oxidant, peroxynitrous acid (ONOOH), either as a bolus or formed at low levels in a time-dependent manner from SIN-1, impairs the capability of AN to polymerize FN. In contrast, exposure of FN to ONOOH does not seem to affect superfibronectin formation to the same extent. This oxidant-induced loss-of-function in AN occurs in a dose-dependent manner, and correlates with structural perturbations, loss of the amino acid tyrosine and tryptophan, and dose-dependent formation of modified amino acid side-chains (3-nitrotyrosine, di-tyrosine and 6-nitrotryptophan). Reagent ONOOH also induces formation of oligomeric species which decrease in the presence of bicarbonate, whereas SIN-1 mainly generates dimers. Modifications were detected at sub-stoichiometric (0.1-fold), or greater, molar excesses of oxidant compared to AN. These species have been localized to specific sites by peptide mass mapping. With high levels of oxidant (>100 times molar excess), ONOOH also induces unfolding of the beta-sheet structure of AN, thermal destabilization, and formation of high molecular mass aggregates. These results have important implications for the understanding of FN fibrillogenesis in vivo, and indicates that AN is highly sensitive to pathophysiological levels of oxidants such as ONOOH.
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Affiliation(s)
- Jianfei He
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Per Hägglund
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
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549
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Chiang WC, Lee MH, Chen TC, Huang JR. Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43's Conformational Transition. Int J Mol Sci 2020; 21:ijms21165930. [PMID: 32824743 PMCID: PMC7460674 DOI: 10.3390/ijms21165930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 12/28/2022] Open
Abstract
Most biological functions involve protein-protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43's IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2's IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other's functions through their IDRs.
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Affiliation(s)
- Wan-Chin Chiang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Ming-Hsuan Lee
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Tsai-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Jie-rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
- Institute of Biomedical Informatics, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan
- Correspondence:
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550
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Haridhasapavalan KK, Sundaravadivelu PK, Thummer RP. Codon Optimization, Cloning, Expression, Purification, and Secondary Structure Determination of Human ETS2 Transcription Factor. Mol Biotechnol 2020; 62:485-494. [PMID: 32808171 DOI: 10.1007/s12033-020-00266-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 02/08/2023]
Abstract
Transcription factor ETS2 regulates genes involved in development, differentiation, angiogenesis, proliferation, and apoptosis. In addition, it is one of the core reprogramming factors responsible for the generation of human cardiomyocytes from adult somatic cells. In this study, we report the heterologous expression of human ETS2 in E. coli to produce a highly pure recombinant protein. To accomplish this, the codon-optimized 1507 bp coding sequence of the human ETS2 gene in fusion with a His-tag, a cell-penetrating peptide, and a nuclear localization sequence was cloned in the protein expression vector and transformed into E. coli strain BL21(DE3) for expression. The recombinant protein was purified to homogeneity under native conditions using immobilized metal ion affinity chromatography, and its identity was confirmed by Western blotting with an ETS2 antibody. Using far-UV circular dichroism spectroscopy, we have demonstrated that the recombinant protein has retained its secondary structure, predominantly comprising of random coils and β-sheets. Prospectively, this biological recombinant ETS2 protein can substitute viral and genetic forms of ETS2 in a cell reprogramming process to facilitate the generation of clinical-grade cells. It can also be used to investigate its molecular role in various biological processes and diseases and for biochemical and structural studies.
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Affiliation(s)
- Krishna Kumar Haridhasapavalan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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