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Shad M, Rehman HM, Akhtar MW, Sajjad M. Structural and functional insights of starch processing α-amylase from hyperthermophilic archaeon Pyrococcusabyssi. Carbohydr Res 2024; 539:109122. [PMID: 38657354 DOI: 10.1016/j.carres.2024.109122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/26/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
The genomic screening of hyper-thermophilic Pyrococcus abyssi showed uncharacterized novel α-amylase sequences. Homology modelling analysis revealed that the α-amylase from P. abyssi consists of an N-terminal GH57 catalytic domain, α-amylase central, and C-terminal domain. Current studies emphasize in-silico structural and functional analysis, recombinant expression, characterization, structural studies through CD spectroscopy, and ligand binding studies of the novel α-amylase from P. abyssi. The soluble expression of PaAFG was observed in the E. coli Rosetta™ (DE3) pLysS strain upon incubation overnight at 18 °C in an orbital shaker. The optimum temperature and pH of the PaAFG were observed at 90 °C in 50 mM phosphate buffer pH 6. The Km value for PaAFG against wheat starch was determined as 0.20 ± 0.053 mg while the corresponding Vmax value was 25.00 ± 0.67 μmol min-1 mg-1 in the presence of 2 mM CaCl2 and 12.5 % glycerol. The temperature ramping experiments through CD spectroscopy reveal no significant change in the secondary structures and positive and negative ellipticities of the CD spectra showing the proper folding and optimal temperature of PaAFG protein. The RMSD and RMSF of the PaAFG enzyme determined through molecular dynamic simulation show the significant protein's stability and mobility. The soluble production, thermostability and broad substrate specificity make this enzyme a promising choice for various industrial applications.
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Affiliation(s)
- Mohsin Shad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan; Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan
| | - Muhammad Waheed Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan.
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Leilabadi-Asl A, Divsalar A, Zare Karizak A, Fateminasab F, Shityakov S, Eslami Moghadam M, Saboury AA. Unraveling the binding interactions between two Pt(II) complexes of aliphatic glycine derivatives with human serum albumin: A comprehensive computational and multi-spectral investigation. Int J Biol Macromol 2024; 266:131298. [PMID: 38574913 DOI: 10.1016/j.ijbiomac.2024.131298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
This article delves into the interaction between HSA protein and synthesized platinum complexes, with formula: [Pt(Propyl-NH2)2(Propylglycine)]NO3 and [Pt(Tertpentyl-NH2)2(Tertpentylglycine)]NO3, through a range of methods, including spectroscopic (UV-visible, fluorescence, synchronous fluorescence and CD) analysis and computational modeling (molecular docking and MD simulation). The binding constants, the number of binding sites, and thermodynamic parameters were obtained at 25 to 37 °C. The study found that both complexes could bind with HSA (moderate affinity for Tertpentyl and strong affinity for Propyl derivatives) and occupied one binding site in HSA (validated with, Stern-Volmer, Job-plots, and molecular docking investigations) located in subdomain IIA. The binding mechanisms of both mentioned Pt(II) agents were different, with the Propyl derivative predominantly using van der Waals forces and hydrogen bond interactions with a static quenching mechanism and the Tertpentyl derivative mainly utilizing hydrophobic force with a dynamic quenching mechanism. However, the two ligands affected protein differently; the Tertpentyl complex did not significantly alter the protein structure upon binding, as evidenced by synchronous fluorescence spectroscopy (SFS), CD spectroscopy, and MD analysis. The outcome helps in understanding the binding mechanisms and structural modifications induced by the ligands, which could aid in the innovation of more effective and stable Pt(II)-based drugs.
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Affiliation(s)
- Amineh Leilabadi-Asl
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Adeleh Divsalar
- Department of Cell & Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Ashkan Zare Karizak
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Fatemeh Fateminasab
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran
| | - Sergey Shityakov
- ITMO University, Infochemistry Scientific Center, Division of Chemoinformatics, Saint-Petersburg 191002, Russian Federation
| | | | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Agrawal A, Varshney R, Gattani A, Kirthika P, Gupta R, Kumar D, Singh RP, Singh P. SLAM (CD150) receptor homologous peptides block the peste des petits ruminants virus entry into B95a cells. Proteins 2024; 92:356-369. [PMID: 37881117 DOI: 10.1002/prot.26595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/19/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023]
Abstract
The fusion of haemagglutinin-neuraminidase (HN) protein of peste des petits ruminant (PPR) virus with signaling lymphocyte activation molecules (SLAM) host cell receptor consequences the virus entry and multiplication inside the host cell. The use of synthetic SLAM homologous peptides (i.e., molecular decoy for HN protein of PPR virus) may check PPR infection at the preliminary stage. Hence, the predicted SLAM homologous peptides using bioinformatics tools were synthesized by solid phase chemistry with standard Merrifield's 9-fluorenylmethoxycarbonyl (Fmoc) chemistry and were purified by reverse phase high performance liquid chromatography. The secondary structures of synthesized peptides were elucidated by circular dichroism spectroscopy. The in vitro interactions of these peptides were studied through indirect Enzyme Linked Immuno Sorbent Assay (ELISA) and visual surface plasmon UV-visible spectroscopy. The SLAM homologous peptides were able to interact with the peste des petits ruminant virus (PPRV) with varying binding efficiency. The interaction of SLAM homologous peptide with the PPR virus was ascertained by the change in the plasmon color from red wine to purple during visual detection and also by bathochromic shift in absorbance spectra under UV-visible spectrophotometry. The cytotoxic and anti-PPRV effect of these peptides were also evaluated in B95a cell line using PPR virus (Sungri/96). The cytotoxic concentration 50 (CC50 ) value of each peptide was greater than 1000 μg mL-1 . The anti-PPRV efficiency of SLAM-22 was relatively high among SLAM homologous peptides, SLAM-22 at 25 μg mL-1 concentration showed a reduction of more than log10 3 virus titer by priming of B95a cell line while the use of SLAM-15 and Muco-17 at the same concentration dropped virus titer from log10 4.8 to log10 2.5 and log10 3.1 respectively. The concentration of SLAM homologous peptide (25 μg mL-1 ) to exert its anti-PPRV effect was much less than its CC50 level (>1000 μg mL-1 ). Therefore, the synthetic SLAM homologous peptides may prove to be better agents to target PPRV.
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Affiliation(s)
- Aditya Agrawal
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal Husbandry, Rewa, Madhya Pradesh, India
| | - Rajat Varshney
- Department of Veterinary Microbiology, Faculty of Veterinary and Animal Sciences, Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India
- Division of Bacteriology and Mycology, ICAR-IVRI, Bareilly, Uttar Pradesh, India
| | - Anil Gattani
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Veterinary Biochemistry, NDVSU, Jabalpur, Madhya Pradesh, India
| | - Perumalraja Kirthika
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rohini Gupta
- Department of Veterinary Medicine, NDVSU, Jabalpur, Madhya Pradesh, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, Uttar Pradesh, India
| | | | - Praveen Singh
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Biophysics Section, ICAR-IVRI, Bareilly, Uttar Pradesh, India
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Bortolus M, Kotynia A, Saielli G, Ruzza P, Di Valentin M, Carraro M, Brasuń J. Detailed investigation of the binding abilities of the heterodomain of a multiHis cyclopeptide toward Cu(II) ions. J Pept Sci 2024:e3568. [PMID: 38317295 DOI: 10.1002/psc.3568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 01/06/2024] [Indexed: 02/07/2024]
Abstract
Cyclopeptides hold significant relevance in various fields of science and medicine, due to their unique structural properties and diverse biological activities. Cyclic peptides, characterized by intrinsically higher conformational order, exhibit remarkable stability and resistance to proteolytic degradation, making them attractive candidates for developing targeted drug delivery systems. The aim of this work is to elucidate the unique coordination properties of the multi-His cyclic peptide with c(HDHKHPHHKHHP) sequence (HDCP - heterodomain cyclopeptide). This peptide, indeed, is able to form homo- and hetero-dinuclear complexes in a wide pH range, being thus a good chelator for Cu(II) ions. Herein, we present the results of a combined study, involving potentiometric, spectroscopic (UV-Vis, CD, and EPR), and computational investigations, on its coordination properties. To better understand the interaction pattern with Cu(II) metal ions, two other peptides, each one bearing only one of the two binding domains of HDCP are also considered in this study: c(HDHKHPGGKGGP) = CP1, c(GKGGKPHHKHHP) = CP2, which share sequence fragments of HDCP and allow separate investigations of its coordination domains.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Aleksandra Kotynia
- Department of Basic Chemical Sciences, Wroclaw Medical University, Wroclaw, Poland
| | - Giacomo Saielli
- Department of Chemical Sciences, University of Padova, Padova, Italy
- Padova Unit, Institute on Membrane Technology of CNR, Padova, Italy
| | - Paolo Ruzza
- Padova Unit, Institute of Biomolecular Chemistry of CNR, Padova, Italy
| | | | - Mauro Carraro
- Department of Chemical Sciences, University of Padova, Padova, Italy
- Padova Unit, Institute on Membrane Technology of CNR, Padova, Italy
| | - Justyna Brasuń
- Department of Basic Chemical Sciences, Wroclaw Medical University, Wroclaw, Poland
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Kotynia A, Krzyżak E, Żądło J, Witczak M, Szczukowski Ł, Mucha J, Świątek P, Marciniak A. Anti-Inflammatory and Antioxidant Pyrrolo[3,4- d]pyridazinone Derivatives Interact with DNA and Bind to Plasma Proteins-Spectroscopic and In Silico Studies. Int J Mol Sci 2024; 25:1784. [PMID: 38339061 PMCID: PMC10855066 DOI: 10.3390/ijms25031784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin.
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Affiliation(s)
- Aleksandra Kotynia
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Edward Krzyżak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Julia Żądło
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Maja Witczak
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Łukasz Szczukowski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Jakub Mucha
- Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland;
| | - Piotr Świątek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Aleksandra Marciniak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
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Lakshmanan RV, Agbandje-McKenna M, McKenna R. Feasibility of Domain Segmentation of B19V VP1u Using Intein Technology for Structural Studies. Protein Pept Lett 2024; 31:PPL-EPUB-137290. [PMID: 38243925 DOI: 10.2174/0109298665277211231214065419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 01/22/2024]
Abstract
INTRODUCTION Parvovirus B19 (B19V) is a human pathogen, and the minor capsid protein of B19V possesses a unique N terminus called VP1u that plays a crucial role in the life cycle of the virus. OBJECTIVE The objective of this study was to develop a method for domain segmentation of B19 VP1u using intein technology, particularly its receptor binding domain (RBD) and phospholipase A2 (PLA2 ) domain. METHODS RBD and PLA2 domains of VP1u were each fused to the DnaE split inteins derived from the Nostoc punctiforme. Each of these precursor proteins was expressed in E. coli. Combining the purified precursors in equal molar ratios resulted in the formation of full-length VP1u. Furthermore, Circular Dichroism (CD) spectroscopy and PLA2 assays were used to probe the structure and activity of the newly formed protein. RESULTS The CD spectrum of the full length VP1u confirmed the secondary structure of protein, while the PLA2 assay indicated minimal disruption in enzymatic activity. CONCLUSION This method would allow for the selective incorporation of NMR-active isotopes into either of the VP1u domains, which can reduce signal overlap in NMR structural determination studies.
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Affiliation(s)
- Renuk Varayil Lakshmanan
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
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Ivanović M, Knez Ž, Leitgeb M. Influence of Supercritical Carbon Dioxide on the Activity and Conformational Changes of α-Amylase, Lipase, and Peroxidase in the Solid State Using White Wheat Flour as an Example. Foods 2023; 12:4499. [PMID: 38137304 PMCID: PMC10743174 DOI: 10.3390/foods12244499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Green technologies using renewable and alternative sources, including supercritical carbon dioxide (sc-CO2), are becoming a priority for researchers in a variety of fields, including the control of enzyme activity which, among other applications, is extremely important in the food industry. Namely, extending shelf life of e.g., flour could be reached by tuning the present enzymes activity. In this study, the effect of different sc-CO2 conditions such as temperature (35-50 °C), pressure (200 bar and 300 bar), and exposure time (1-6 h) on the inactivation and structural changes of α-amylase, lipase, and horseradish peroxidase (POD) from white wheat flour and native enzymes was investigated. The total protein (TPC) content and residual activities of the enzymes were determined by standard spectrophotometric methods, while the changes in the secondary structures of the enzymes were determined by circular dichroism spectrometry (CD). The present work is therefore concerned for the first time with the study of the stability and structural changes of the enzyme molecules dominant in white wheat flour under sc-CO2 conditions at different pressures and temperatures. In addition, the changes in aggregation or dissociation of the enzyme molecules were investigated based on the changes in particle size distribution and ζ-potential. The results of the activity assays showed a decrease in the activity of native POD and lipase under optimal exposure conditions (6 h and 50 °C; and 1 h and 50 °C) by 22% and 16%, respectively. In contrast, no significant changes were observed in α-amylase activity. Consequently, analysis of the CD spectra of POD and lipase confirmed a significant effect on secondary structure damage (changes in α-helix, β-sheet, and β-turn content), whereas the secondary structure of α-amylase retained its original configuration. Moreover, the changes in particle size distribution and ζ-potential showed a significant effect of sc-CO2 treatment on the aggregation and dissociation of the selected enzymes. The results of this study confirm that sc-CO2 technology can be effectively used as an environmentally friendly technology to control the activity of major flour enzymes by altering their structures.
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Affiliation(s)
- Milena Ivanović
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
| | - Željko Knez
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Maja Leitgeb
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
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Boissieras J, Granzhan A. Potentiometric titrations to study ligand interactions with DNA i-motifs. Methods Enzymol 2023; 695:233-254. [PMID: 38521587 DOI: 10.1016/bs.mie.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
i-Motifs are non-canonical secondary structures of DNA formed by mutual intercalation of hemi-protonated cytosine-cytosine base pairs, most typically in slightly acidic conditions (pH<7.0). These structures are well-studied in vitro and have recently been suggested to exist in cells. Despite nearly a decade of active research, the quest for small-molecule ligands that could selectively bind to and stabilize i-motifs continues, and no reference, bona fide i-motif ligand is currently available. This is, at least in part, due to the lack of robust methods to assess the interaction of ligands with i-motifs, since many techniques well-established for studies of other secondary structures (such as CD-, UV-, and FRET-melting) may generate artifacts when applied to i-motifs. Here, we describe an implementation of automated, potentiometric (pH) titrations as a robust isothermal method to assess the impact of ligands or cosolutes on thermodynamic stability of i-motifs. This approach is validated through the use of a cosolute previously known to stabilize i-motifs (PEG2000) and three small-molecule ligands that are able to stabilize, destabilize, or have no effect on the stability of i-motifs, respectively.
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Affiliation(s)
- Joseph Boissieras
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France
| | - Anton Granzhan
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France.
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Agrawal A, Varshney R, Gattani A, Hira Khan M, Gupta R, Solanki KS, Patel SK, Singh RP, Singh P. Development of Hemagglutinin-Neuraminidase Homologous Peptides as Novel Promising Therapeutic Agents Against Peste des Petits Ruminants Virus. Protein J 2023; 42:685-697. [PMID: 37421558 DOI: 10.1007/s10930-023-10134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
The lack of specific antiviral therapy and complications associated with the existing peste des petits ruminants (PPR) vaccines accentuates the search of novel antiviral blocking agents in order to curtail the PPR infection at initial level. The synthetic hemagglutinin-neuraminidase (HN) homologous peptides may compete with the natural HN protein of PPR virus for binding to signaling lymphocytic activation molecule (SLAM) receptor, consequently, may disrupt peste des petits ruminants virus (PPRV) at entry level. Therefore, insilico analysis, synthesis, purification and subsequent characterization of HN homologous peptides were conducted in this study. The HN homologous peptides were synthesized by means of solid phase chemistry and were purified by reversed-phase-high performance liquid chromatography. The mass as well as sequence of HN homologous peptides were assessed by mass spectroscopy while its secondary structure was elucidated by circular dichroism spectroscopy. The binding (interaction) efficacy of HN homologous peptides with PPRV antibodies was assessed via indirect enzyme linked immunosorbent assay, visual detection test (red wine to purple), bathochromic shift under UV-Vis spectrophotometry and lateral flow immunochromatographic strip test. The antiviral properties and cytotoxicity of these peptides were also assessed in B95a cell line with changes in cytopathic effect and titer of PPRV (Sungri/96). The presence of green fluorescein isothiocyanate over the B95a cell surface pointed towards the binding of HN homologous peptides with surface SLAM receptor. Moreover, the intact beta sheet configuration in water and lower cytotoxicity [cytotoxic concentration 50 (CC50) > 1000 µg/ml] of these peptides signifies its in vivo use. Among HN homologous peptides, the binding efficacy and antiviral properties of pep A was relatively high in comparison to pep B and Pep ppr peptides. The prerequisite concentration of HN homologous peptides (pep A = 12.5 µg/ml; pep B = 25 µg/ml; pep ppr = 25 µg/ml) to exemplify its antiviral effect was much lower than its CC50 level. Hence, this study signifies the therapeutic potential of synthetic HN homologous peptides.
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Affiliation(s)
- Aditya Agrawal
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India.
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Rewa, Jabalpur, 486001, India.
| | - Rajat Varshney
- Department of Veterinary Microbiology, BHU, Mirzapur, U.P., 231001, India
- Division of Bacteriology and Mycology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Anil Gattani
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Mahvash Hira Khan
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Rohini Gupta
- Department of Veterinary Medicine, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Khushal Singh Solanki
- Division of Veterinary Biotechnology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Shailesh Kumar Patel
- Department of Veterinary Pathology, College of Veterinary Science and Animal husbandry, NDVSU, Rewa, Jabalpur, 486001, India
| | - R P Singh
- Division of Bacteriology and Mycology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Praveen Singh
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
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10
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Kost V, Sukhov D, Ivanov I, Kasheverov I, Ojomoko L, Shelukhina I, Mozhaeva V, Kudryavtsev D, Feofanov A, Ignatova A, Utkin Y, Tsetlin V. Comparison of Conformations and Interactions with Nicotinic Acetylcholine Receptors for E. coli-Produced and Synthetic Three-Finger Protein SLURP-1. Int J Mol Sci 2023; 24:16950. [PMID: 38069271 PMCID: PMC10707033 DOI: 10.3390/ijms242316950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
SLURP-1 is a three-finger human protein targeting nicotinic acetylcholine receptors (nAChRs). The recombinant forms of SLURP-1 produced in E. coli differ in added fusion fragments and in activity. The closest in sequence to the naturally occurring SLURP-1 is the recombinant rSLURP-1, differing by only one additional N-terminal Met residue. sSLURP-1 can be prepared by peptide synthesis and its amino acid sequence is identical to that of the natural protein. In view of recent NMR analysis of the conformational mobility of rSLURP-1 and cryo-electron microscopy structures of complexes of α-bungarotoxin (a three-finger snake venom protein) with Torpedo californica and α7 nAChRs, we compared conformations of sSLURP-1 and rSLURP-1 by Raman spectroscopy and CD-controlled thermal denaturation, analyzed their competition with α-bungarotoxin for binding to the above-mentioned nAChRs, compared the respective receptor complexes with computer modeling and compared their inhibitory potency on the α9α10 nAChR. The CD revealed a higher thermostability of sSLURP-1; some differences between sSLURP-1 and rSLURP-1 were observed in the regions of disulfides and tyrosine residues by Raman spectroscopy, but in binding, computer modeling and electrophysiology, the proteins were similar. Thus, sSLURP-1 and rSLURP-1 with only one additional Met residue appear close in structure and functional characteristics, being appropriate for research on nAChRs.
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Affiliation(s)
- Vladimir Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Dmitry Sukhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Igor Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Igor Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Lucy Ojomoko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Irina Shelukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Vera Mozhaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Denis Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya Str., 119048 Moscow, Russia
| | - Alexey Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Anastasia Ignatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Yuri Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
| | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.K.); (D.S.); (I.I.); (I.K.); (L.O.); (I.S.); (V.M.); (D.K.); (A.F.); (Y.U.)
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11
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Szeltner Z, Ferenc G, Juhász T, Kupihár Z, Váradi Z, Szüts D, Kovács L. Probing telomeric-like G4 structures with full or partial 2'-deoxy-5-hydroxyuridine substitutions. Biochimie 2023; 214:33-44. [PMID: 36707016 DOI: 10.1016/j.biochi.2023.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 01/14/2023] [Indexed: 01/26/2023]
Abstract
Guanine quadruplexes (G4s) are stable four-stranded secondary DNA structures held together by noncanonical G-G base tetrads. We synthesised the nucleoside analogue 2'-deoxy-5-hydroxyuridine (H) and inserted its phosphoramidite into telomeric repeat-type model oligonucleotides. Full and partial substitutions were made, replacing all guanines in all the three tetrads of a three-tier G4 structure, or only in the putative upper, central, or lower tetrads. We characterised these modified structures using CD, UV absorbance spectroscopy, native gel studies, and a capture oligo-based G4 disruption kinetic assay. The strand separation activity of BLM helicase on these substituted structures was also investigated. Two of the partially H-substituted constructs adopted G4-like structures, but displayed lower thermal stabilities compared to unsubstituted G4. The construct modified in its central tetrad remained mostly denatured, but the possibility of a special structure for the fully replaced variant remained open. H substitutions did not interfere with the G4-resolving activity of BLM helicase, but its efficiency was highly influenced by construct topology and even more by the G4 ligand PhenDC3. Our results suggest that the H modification can be incorporated into G quadruplexes, but only at certain positions to maintain G4 stability. The destabilizing effect observed for 2'-deoxy-5-hydroxyuridine indicates that the cytosine deamination product 5-hydroxyuracil and its nucleoside counterpart in RNA (5-hydroxyuridine), might also be destabilizing in cellular DNA and RNA quadruplexes. The kinetic assay employed in this study can be generally employed for a fast comparison of the stabilities of various G4s either in their free or ligand-bound states.
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Affiliation(s)
- Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, Eötvös Loránd Research Network, Temesvári Krt. 62, H-6726, Szeged, Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary
| | - Zoltán Kupihár
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary
| | - Zoltán Váradi
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary.
| | - Lajos Kovács
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary.
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12
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Warthegau SS, Hillers-Bendtsen AE, Pedersen SK, Rindom C, Braestrup C, Jensen JS, Hammerich O, Thomsen MS, Kamounah FS, Norman P, Mikkelsen KV, Brock-Nannestad T, Pittelkow M. Heterocyclic [9]Helicenes Exhibiting Bright Circularly Polarized Luminescence. Chemistry 2023; 29:e202301815. [PMID: 37458527 DOI: 10.1002/chem.202301815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
We describe a concise synthetic strategy for the preparation of heterocyclic [9]helicenes and a simple preparative-scale protocol for the optical resolution of the resulting M- and P-enantiomers. The helicenes were characterized by single-crystal X-ray diffraction along with a range of spectroscopic and computational techniques. A fluorescence quantum yield of up to 65 % was observed, and the chiroptical properties of both M- and P-helicenes revealed large dissymmetry factors. The circularly polarized luminescence brightness reaches up to 17 M-1 cm-1 , as measured experimentally and verified computationally, which makes this the highest circularly polarized luminescence brightness among heterocyclic helicenes. We describe how chiroptical properties (both circular dichroism and circularly polarized luminescence) can be described and predicted using quantum chemical calculations. The synthetic approach also reveals by-products that originate from internal oxidation reactions, presumably mediated by the close proximity of the π-surfaces in the helicene structure.
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Affiliation(s)
- Stefan S Warthegau
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | | | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Cecilie Rindom
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Christoffer Braestrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Jeppe S Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Ole Hammerich
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Maria S Thomsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Theis Brock-Nannestad
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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13
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Schultz KM, Schneider JR, Fischer MA, Cina NP, Riegert MO, Frank DW, Klug CS. Binding and transport of LPS occurs through the coordinated combination of an array of sites across the entire E. coli LPS transport protein LptA. Protein Sci 2023:e4724. [PMID: 37417889 PMCID: PMC10360375 DOI: 10.1002/pro.4724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
The outer leaflet of the outer membrane (OM) of bacteria such as Escherichia coli, Pseudomonas aeruginosa, and other important pathogens is largely composed of lipopolysaccharide (LPS), which is essential to nearly all Gram-negative bacteria. LPS is transported to the outer leaflet of the OM through a yet unknown mechanism by seven proteins that comprise the LPS transport system. LptA, the only entirely periplasmic Lpt protein, bridges the periplasmic space between the IM LptB2 FGC and the OM LptDE complexes. LptA is postulated to protect the hydrophobic acyl chains of LPS as it crosses the hydrophilic periplasm, is essential to cell viability, and contains many conserved residues distributed across the protein. To identify which side chains are required for function of E. coli LptA in vivo, we performed a systematic, unbiased, high-throughput screen of the effect of 172 single alanine substitutions on cell viability utilizing an engineered BL21 derivative with a chromosomal knockout of the lptA gene. Remarkably, LptA is highly tolerant to amino acid substitution with alanine. Only four alanine mutants could not complement the chromosomal knockout; CD spectroscopy showed that these substitutions resulted in proteins with significantly altered secondary structure. In addition, 29 partial loss-of-function mutants were identified that led to OM permeability defects; interestingly, these sites were solely located within β-strands of the central core of the protein and each resulted in misfolding of the protein. Therefore, no single residue within LptA is responsible for LPS binding, supporting previous EPR spectroscopy data indicating that sites across the entire protein work in concert to bind and transport LPS. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kathryn M Schultz
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - John R Schneider
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Matthew A Fischer
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Nicholas P Cina
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Molly O Riegert
- Department of Microbiology & Immunology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Dara W Frank
- Department of Microbiology & Immunology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
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14
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Boudko SP, Konopka EH, Kim W, Taga Y, Mizuno K, Springer TA, Hudson BG, Moy TI, Lin FY. A recombinant technique for mapping functional sites of heterotrimeric collagen helices: Collagen IV CB3 fragment as a prototype for integrin binding. J Biol Chem 2023; 299:104901. [PMID: 37302550 PMCID: PMC10404678 DOI: 10.1016/j.jbc.2023.104901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Collagen superfamily of proteins is a major component of the extracellular matrix. Defects in collagens underlie the cause of nearly 40 human genetic diseases in millions of people worldwide. Pathogenesis typically involves genetic alterations of the triple helix, a hallmark structural feature that bestows exceptional mechanical resistance to tensile forces and a capacity to bind a plethora of macromolecules. Yet, there is a paramount knowledge gap in understanding the functionality of distinct sites along the triple helix. Here, we present a recombinant technique to produce triple helical fragments for functional studies. The experimental strategy utilizes the unique capacity of the NC2 heterotrimerization domain of collagen IX to drive three α-chain selection and registering the triple helix stagger. For proof of principle, we produced and characterized long triple helical fragments of collagen IV that were expressed in a mammalian system. The heterotrimeric fragments encompassed the CB3 trimeric peptide of collagen IV, which harbors the binding motifs for α1β1 and α2β1 integrins. Fragments were characterized and shown to have a stable triple helix, post-translational modifications, and high affinity and specific binding of integrins. The NC2 technique is a universal tool for the high-yield production of heterotrimeric fragments of collagens. Fragments are suitable for mapping functional sites, determining coding sequences of binding sites, elucidating pathogenicity and pathogenic mechanisms of genetic mutations, and production of fragments for protein replacement therapy.
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Affiliation(s)
- Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
| | | | - Woojin Kim
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Yuki Taga
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Billy G Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Terence I Moy
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Fu-Yang Lin
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA.
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15
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Johnson KL, Graves AB, Eckhert K, Liptak MD. Second-sphere tuning of analogues for the ferric-hydroperoxoheme form of Mycobacterium tuberculosis MhuD. J Inorg Biochem 2023; 246:112300. [PMID: 37364353 DOI: 10.1016/j.jinorgbio.2023.112300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Mycobacterium tuberculosis MhuD catalyzes the oxygenation of heme to mycobilin; experimental data presented here elucidates the novel hydroxylation reaction catalyzed by this enzyme. Analogues for the critical ferric-hydroperoxoheme (MhuD-heme-OOH) intermediate of this enzyme were characterized using UV/Vis absorption (Abs), circular dichroism (CD), and magnetic CD (MCD) spectroscopies. In order to extract electronic transition energies from these spectroscopic data, a novel global fitting model was developed for analysis of UV/Vis Abs, CD, and MCD data. A variant of MhuD was prepared, N7S, which weakens the affinity of heme-bound enzyme for a hydroperoxo analogue, azide, without significantly altering the protein secondary structure. Global fitting of spectroscopic data acquired in this study revealed that the second-sphere N7S substitution perturbs the electronic structure of two analogues for MhuD-heme-OOH: azide-inhibited MhuD (MhuD-heme-N3) and cyanide-inhibited MhuD (MhuD-heme-CN). The ground state electronic structures of MhuD-heme-N3 and MhuD-heme-CN were assessed using variable-temperature, variable-field MCD. Altogether, these data strongly suggest that there is a hydrogen bond between the Asn7 side-chain and the terminal oxygen of the hydroperoxo ligand in MhuD-heme-OOH. As discussed herein, this finding supports a novel hydroxylation reaction mechanism where the Asn7 side-chain guides a transient hydroxyl radical derived from homolysis of the OO bond in MhuD-heme-OOH to the β- or δ-meso carbon of the porphyrin ligand yielding β- or δ-meso-hydroxyheme, respectively.
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Affiliation(s)
- Kayla L Johnson
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Amanda B Graves
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Kaitlyn Eckhert
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America.
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16
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Zhang L, Guan Q, Tang L, Jiang J, Sun K, Manirafasha E, Zhang M. Effect of Cu 2+ and Al 3+ on the interaction of chlorogenic acid and caffeic acid with serum albumin. Food Chem 2023; 410:135406. [PMID: 36610087 DOI: 10.1016/j.foodchem.2023.135406] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/25/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Despite the phenolic acids' health benefits, their interactions with proteins are still unclear. In this study, the interactions of Bovine Serum Albumin (BSA) with chlorogenic acid (CHA), caffeic acid (CA), and their Al3+, Cu2+ complexes were studied by using circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and UV/Vis spectroscopy. It was found that esterification of carboxyl group of CA with quinic acid increased the binding affinities for BSA. After chelating with Cu2+ and Al3+, both CHA and CA exhibited high binding affinities for BSA. CHA could form CHA-Cu2 and CHA-Al2 complex with Cu2+ and Al3+. The result of CD spectroscopy demonstrated that the binding of CHA and Al3+ with BSA contributed to the folding of BSA secondary structure. In addition, with the presence of CHA, binding with Al3+ could also induce changes in BSA conformation. The binding sites of both CHA and CA were closed to Trp213.
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Affiliation(s)
- Liangliang Zhang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen 361021, China.
| | - Qinhao Guan
- Institute of Chemical Industry of Forest Products, CAF, Nanjing 210042, China
| | - Lihuan Tang
- Institute of Chemical Industry of Forest Products, CAF, Nanjing 210042, China
| | - Jianchun Jiang
- Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen 361021, China; Institute of Chemical Industry of Forest Products, CAF, Nanjing 210042, China
| | - Kang Sun
- Institute of Chemical Industry of Forest Products, CAF, Nanjing 210042, China
| | - Emmanuel Manirafasha
- University of Rwanda-College of Education, Rukara Campus Eastern Province, Po Box: 55 Rwamagana-Eastern Province, Kigali, Rwanda
| | - Meng Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
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17
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Osetrina DA, Kusova AM, Bikmullin AG, Klochkova EA, Yulmetov AR, Semenova EA, Mukhametzyanov TA, Usachev KS, Klochkov VV, Blokhin DS. Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation. Int J Mol Sci 2023; 24:ijms24108949. [PMID: 37240295 DOI: 10.3390/ijms24108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.
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Affiliation(s)
- Daria A Osetrina
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Aleksandra M Kusova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan 420111, Russia
| | - Aydar G Bikmullin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Evelina A Klochkova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Aydar R Yulmetov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Evgenia A Semenova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Timur A Mukhametzyanov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Konstantin S Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan 420111, Russia
| | - Vladimir V Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Dmitriy S Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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18
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Grabowska O, Samsonov SA, Chmurzyński L, Wyrzykowski D, Żamojć K. Investigation of hexacyanoferrate(II)/(III) charge-dependent interactions with bovine and human serum albumins. Spectrochim Acta A Mol Biomol Spectrosc 2023; 293:122505. [PMID: 36809739 DOI: 10.1016/j.saa.2023.122505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/21/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
In the present paper, the binding interactions of highly negative-charged ions, namely hexacyanoferrates(II/III), i.e. [Fe(CN)6]4- and [Fe(CN)6]3- with bovine and human serum albumins (BSA and HSA, respectively) have been studied for the first time in an aqueous solution (10 mM cacodylate buffer of pH 7.0) using steady-state fluorescence spectroscopy, isothermal titration calorimetry, and CD spectroscopy supported by molecular dynamics-based computational approaches. The Stern-Volmer equation as well as its modifications suggested that hexacyanoferrates(II/III) effectively quenched the intrinsic fluorescence of the albumins through a static mechanism. The proteins under study possess only one binding site on the surface capable of binding one mole of hexacyanoferrates(II/III) ions per one mole of albumin (HSA or BSA). The formation of albumin complexes is an enthalpy-driven process (|ΔHITC| > |TΔSITC|). The strength of the interactions depends mainly on the type of albumin, and changes as follows: BSA-K3[Fe(CN)6] ∼ BSA-K4[Fe(CN)6] > HSA-K3[Fe(CN)6] ∼ HSA-K4[Fe(CN)6]. Finally, potential binding sites of bovine and human serum albumins have been investigated and discussed based on a competitive fluorescence displacement assay (with warfarin and ibuprofen as site markers) and molecular dynamics simulations.
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Affiliation(s)
- Ola Grabowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lech Chmurzyński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Krzysztof Żamojć
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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19
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Cantini F, Giannì P, Bobone S, Troiano C, van Ingen H, Massoud R, Perini N, Migliore L, Savarin P, Sanders C, Stella L, Sette M. Structural and Functional Characterization of the Newly Designed Antimicrobial Peptide Crabrolin21. Membranes (Basel) 2023; 13:365. [PMID: 36984752 PMCID: PMC10053045 DOI: 10.3390/membranes13030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
(1) Background: antimicrobial resistance is becoming a dramatic problem for public health, and the design of new antimicrobial agents is an active research area. (2) Methods: based on our previous work, we designed an improved version of the crabrolin peptide and characterized its functional and structural properties with a wide range of techniques. (3) Results: the newly designed peptide, crabrolin21, is much more active than the previous ones and shows specific selectivity towards bacterial cells. (4) Conclusions: crabrolin21 shows interesting properties and deserves further studies.
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Affiliation(s)
- Francesca Cantini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, 50019 Firenze, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, 50019 Firenze, Italy
| | - Paola Giannì
- Department of Chemical Sciences and Technology, University of Rome Tor Vergata, 00133 Rome, Italy
- Fondazione G.I.M.EM.A.-Franco Mandelli Onlus, 00182 Rome, Italy
| | - Sara Bobone
- Department of Chemical Sciences and Technology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Cassandra Troiano
- Department of Chemical Sciences and Technology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Renato Massoud
- Department of Experimental Medicine, University of Rome Tor Vergata, Viale della Ricerca Scientifica, 00133 Rome, Italy
| | - Nicoletta Perini
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Luciana Migliore
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, 22060 Novedrate, Italy
| | - Philippe Savarin
- Chemistry Structures Properties of Biomaterials and Therapeutic Agents Laboratory (CSPBAT), Nanomédecine Biomarqueurs Détection Team (NBD), Sorbonne Paris Nord University, The National Center for Scientific Research (CNRS), UMR 7244, 74 Rue Marcel Cachin, CEDEX, 93017 Bobigny, France
| | - Charles Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lorenzo Stella
- Department of Chemical Sciences and Technology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Marco Sette
- Department of Chemical Sciences and Technology, University of Rome Tor Vergata, 00133 Rome, Italy
- Chemistry Structures Properties of Biomaterials and Therapeutic Agents Laboratory (CSPBAT), Nanomédecine Biomarqueurs Détection Team (NBD), Sorbonne Paris Nord University, The National Center for Scientific Research (CNRS), UMR 7244, 74 Rue Marcel Cachin, CEDEX, 93017 Bobigny, France
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20
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Bérczi A, Márton Z, Laskay K, Tóth A, Rákhely G, Duzs Á, Sebők-Nagy K, Páli T, Zimányi L. Spectral and Redox Properties of a Recombinant Mouse Cytochrome b561 Protein Suggest Transmembrane Electron Transfer Function. Molecules 2023; 28:molecules28052261. [PMID: 36903505 PMCID: PMC10005133 DOI: 10.3390/molecules28052261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Cytochrome b561 proteins (CYB561s) are integral membrane proteins with six trans-membrane domains, two heme-b redox centers, one on each side of the host membrane. The major characteristics of these proteins are their ascorbate reducibility and trans-membrane electron transferring capability. More than one CYB561 can be found in a wide range of animal and plant phyla and they are localized in membranes different from the membranes participating in bioenergization. Two homologous proteins, both in humans and rodents, are thought to participate-via yet unidentified way-in cancer pathology. The recombinant forms of the human tumor suppressor 101F6 protein (Hs_CYB561D2) and its mouse ortholog (Mm_CYB561D2) have already been studied in some detail. However, nothing has yet been published about the physical-chemical properties of their homologues (Hs_CYB561D1 in humans and Mm_CYB561D1 in mice). In this paper we present optical, redox and structural properties of the recombinant Mm_CYB561D1, obtained based on various spectroscopic methods and homology modeling. The results are discussed in comparison to similar properties of the other members of the CYB561 protein family.
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Affiliation(s)
- Alajos Bérczi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Zsuzsanna Márton
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Krisztina Laskay
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - András Tóth
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Ágnes Duzs
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Correspondence:
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21
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Abstract
The B-DNA to Z-DNA transition is a remarkable conformational change in DNA, which was originally observed in poly-GC DNA in the presence of high salt concentration. This eventually prompted the observation of the crystal structure of Z-DNA, a left-handed double-helical DNA, at atomic resolution. Despite advances in Z-DNA research, the application of circular dichroism (CD) spectroscopy as the fundamental technique to characterize this unique DNA conformation has remained constant. In this chapter, we describe a CD spectroscopic method for characterizing the B-DNA to Z-DNA transition of a CG-repeat double-stranded DNA fragment formed from a protein or chemical inducer.
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Affiliation(s)
- Vinod Kumar Subramani
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
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22
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Dasari AKR, Lim KH. CD and Solid-State NMR Studies of Low-Order Oligomers of Transthyretin. Methods Mol Biol 2023; 2551:311-320. [PMID: 36310212 DOI: 10.1007/978-1-0716-2597-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Characterization of oligomeric intermediate states populated at an early stage of misfolding and aggregation is essential to understanding molecular mechanism of pathogenic protein aggregation. Growing evidence also suggests that oligomeric species are more toxic than mature fibrillar counterparts. Here, we describe procedures for isolating oligomeric species of an aggregation-prone protein, transthyretin, associated with protein misfolding disorders, including cardiomyopathy and polyneuropathy. We also describe methods for structural studies of the oligomeric species using circular dichroism and solid-state NMR spectroscopy. These methods can be applied to structural characterization of oligomeric intermediates of other aggregation-prone proteins.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, USA.
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23
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Das M, Brandao P, Mati SS, Roy S, Anoop A, James A, De S, Das UK, Laha S, Mondal J, Samanta BC, Maity T. Effect of ancillary ligand on DNA and protein interaction of the two Zn (II) and Co (III) complexes: experimental and theoretical study. J Biomol Struct Dyn 2022; 40:14188-14203. [PMID: 34842505 DOI: 10.1080/07391102.2021.2001377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the present work we have developed one mononuclear Zn(II) complex [Zn(L)(H2O)] (Complex 1) by utilizing a tetracoordinated ligand H2L, formed by simple condensation of 2, 2 dimethyl 1,3 diamino propane and 3- ethoxy salicylaldehyde and one newly designed mononuclear Co (III) complex [Co(L)(L1)] (complex 2) by utilizing (H2L) and 3- ethoxy salicylaldehyde(HL1) as an ancillary ligand. The newly developed complex 2 have been spectroscopically characterized. An interesting phenomenon has been noticed that in presence of ancillary ligand, the solubility in buffer solution and the thermal stability of complex 2 comparatively increases than 1. To check the effect of ancillary ligand, present in complex 2 towards the DNA and HSA binding efficacy, both the complexes have been taken into consideration to inspect their binding potentiality with the macromolecules. The 'on', 'off' fluorescence changes in presence of DNA and HSA, the binding constant values, obtained from electronic spectral titration, iodide induced quenching, competitive binding assay, circular dichroism (CD) spectral titration, time resolved fluorescence experiment unambiguously assure the better binding efficacy of complex 2 with the signal of minor groove binding mode with DNA along with no significant conformational changes of the macromolecules. The strong and spontaneous binding of complex 2 with CT-DNA is further supported by the Isothermal Titration Calorimetry (ITC) study. Furthermore TDDFT calculation of DNA with and without complex 2 significantly authorize the formation of complex 2-DNA adduct during the association. Finally Molecular Docking study properly verifies the experimental findings and provides justified explanation behinds experimental findings.
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Affiliation(s)
- Manik Das
- Department of Chemistry, P. K. College, Contai, India
| | - Paola Brandao
- Departamento de Química/CICEC, Universidade de Aveiro, Aveiro, Portugal
| | - Soumya Sundar Mati
- Department of Chemistry, Government General Degree College, Keshiary, India
| | - Saikat Roy
- Department of Chemistry, IIT Kharagpur, Kharagpur, India
| | | | - Anjima James
- Department of Applied Chemistry, Cochin University of Science and Technology, Cochin, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Cochin, India
| | - Uttam Kumar Das
- Department of Chemistry, School of Physical sciences, Mahatma Gandhi Central University, Motihari, India
| | - Soumik Laha
- Indian Institute of Chemical Biology CSIR, Kolkata, India
| | - Jisu Mondal
- Indian Institute of Chemical Biology CSIR, Kolkata, India
| | | | - Tithi Maity
- Department of Chemistry, P. K. College, Contai, India
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24
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Abstract
A cysteine proteinase inhibitor has been purified by affinity chromatography from the liver of buffalo. Liver cystatin is subjected to incubation at low pH with co-solvent TFE, where we have studied the effect on the conformation, activity and tendency to form aggregates or fibrils. ANS fluorescence was used to study conformational changes. The fibril formation and aggregation was studied using ThT assay, CD, FTIR and fluorescence spectroscopy. At pH 3.0 there was no fibril formation though aggregates were formed but in presence of TFE fibrils appeared. At pH 2.0 and 1.0, TFE induced rapid fibril formation compared to only acid induced state as assessed by Thioflavin T (ThT) fluorescence.TFE stabilized each of the three acid induced intermediates at predenaturational concentrations (20%) and accelerated fibril formation. Solvent conditions had a profound effect on the tendency of liver cystatin to produce fibrils and aggregation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Mustafa Mir
- Department of Biochemistry, faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India.,School of Biotechnology and Graduate school of Biochemistry, Yeungnum University, Gyeongsan, South Korea
| | - Bilqees Bano
- Department of Biochemistry, faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India
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25
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Sanchugova D, Kusova A, Bikmullin A, Yulmetov A, Mukhametzyanov T, Klochkov V, Blokhin D. Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68-107) by NMR spectroscopy and MD simulations. J Struct Biol 2022; 214:107900. [PMID: 36191746 DOI: 10.1016/j.jsb.2022.107900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
SEM1(68-107) is a peptide corresponding to the region of semenogelin 1 protein from 68 to 107 amino acid position. SEM1(68-107) is an abundant component of semen, which participates in HIV infection enhanced by amyloid fibrils forming. To understand the causes influencing amyloid fibril formation, it is necessary to determine the spatial structure of SEM1(68-107). It was shown that the determination of SEM1(68-107) structure is complicated by the non-informative NMR spectra due to the high intramolecular mobility of peptides. The complementary approach based on the geometric restrictions of individual peptide fragments and molecular modeling was used for the determination of the spatial structure of SEM1(68-107). The N- (SEM1(68-85)) and C-terminuses (SEM1(86-107)) of SEM1(68-107) were chosen as two individual peptide fragments. SEM1(68-85) and SEM1(86-107) structures were established with NMR and circular dichroism CD spectroscopies. These regions were used as geometric restraints for the SEM1(68-107) structure modeling. Even though most of the SEM1(68-107) peptide is unstructured, our detailed analysis revealed the following structured elements: N-terminus (70His-84Gln) forms an α-helix, (86Asp-94Thr) and (101Gly-103Ser) regions fold into 310-helixes. The absence of a SEM1(68-107) rigid conformation leads to instability of these secondary structure regions. The calculated SEM1(68-107) structure is in good agreement with experimental values of hydrodynamic radius and dihedral angles obtained by NMR spectroscopy. This testifies the adequacy of a combined approach based on the use of peptide fragment structures for the molecular modeling formation of full-size peptide spatial structure.
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26
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Monti M, Stener M, Aschi M. A computational approach for modeling electronic circular dichroism of solvated chromophores. J Comput Chem 2022; 43:2023-2036. [PMID: 36134712 PMCID: PMC9825941 DOI: 10.1002/jcc.27001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
The present study consists in a novel computational protocol to model the UV-circular dichroism spectra of solvated species. It makes use of quantum-chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG+ and to the aqueous neutral decapeptide (GVGVP)2 . The protocol has proven able to: (i) properly consider the conformational motion of solute in the given environment; (ii) give the actual statistical weight of each conformational state; (iii) provide a reliable quantum mechanical method able to reproduce the spectral features. Temperature effects on conformations and spectral properties are properly taken into account. The role of explicit solvent on the conformational analysis and the spectra calculation is discussed. The comparison of the calculated circular dichroism spectra with experimental ones recorded at different temperatures represents a strict validation test of the method.
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Affiliation(s)
- Marta Monti
- Dipartimento di Scienze Chimiche e FarmaceuticheUniversità di TriesteTriesteItaly
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e FarmaceuticheUniversità di TriesteTriesteItaly
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e ChimicheUniversità dell'AquilaL'AquilaItaly
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27
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Le-Deygen IM, Safronova AS, Kolmogorov IM, Skuredina AA, Kudryashova EV. The Influence of Lipid Matrix Composition on the Microenvironment of Levofloxacin in Liposomal Forms. Russ J Bioorg Chem 2022; 48:710-719. [PMID: 36119964 PMCID: PMC9467668 DOI: 10.1134/s1068162022040148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022]
Abstract
We have studied the interaction of the antibacterial drug levofloxacin with lipid bilayers of various compositions: 100% DPPC and with the addition of 20% cardiolipin. For DPPC liposomes, levofloxacin was found to penetrate into the subpolar region at the lipid-water interface. The role of the anionic lipid in the interaction of an active molecule with a bilayer has been established: levofloxacin enters the microenvironment of the phosphate group, displacing water, and does not penetrate into the hydrophobic part of the bilayer. For the first time, the study of the microenvironment of levofloxacin in the liposome by IR and CD spectroscopy was carried out. Such an approach based on a combination of several spectral methods opens up new prospects for the creation of new medicinal properties and the possibility of predicting the nature of the interaction of active molecules with biomembranes in order to predict their efficacy and potential side effects.
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Affiliation(s)
- I M Le-Deygen
- Chemistry Department, Moscow State University, 199991 Moscow, Russia
| | - A S Safronova
- Chemistry Department, Moscow State University, 199991 Moscow, Russia
| | - I M Kolmogorov
- Chemistry Department, Moscow State University, 199991 Moscow, Russia
| | - A A Skuredina
- Chemistry Department, Moscow State University, 199991 Moscow, Russia
| | - E V Kudryashova
- Chemistry Department, Moscow State University, 199991 Moscow, Russia
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28
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Solov'eva TF, Bakholdina SI, Khomenko VA, Sidorin EV, Kim NY, Novikova OD, Shnyrov VL, Stenkova AM, Eremeev VI, Bystritskaya EP, Isaeva MP. Expression of membrane beta-barrel protein in E. coli at low temperatures: Structure of Yersinia pseudotuberculosis OmpF porin inclusion bodies. Biochim Biophys Acta Biomembr 2022; 1864:183971. [PMID: 35643329 DOI: 10.1016/j.bbamem.2022.183971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The recombinant OmpF porin of Yersinia pseudotuberculosis as a model of transmembrane protein of the β-barrel structural family was used to study low growth temperature effect on the structure of the produced inclusion bodies (IBs). This porin showed a very low expression level in E. coli at a growth temperature below optimal 37 °C. The introduction of a N-terminal hexahistidine tag into the mature porin molecule significantly increased the biosynthesis of the protein at low cultivation temperatures. The recombinant His-tagged porin (rOmpF-His) was expressed in E. coli at 30 and 18 °C as inclusion bodies (IB-30 and IB-18). The properties and structural organization of IBs, as well as the structure of rOmpF-His solubilized from the IBs with urea and SDS, were studied using turbidimetry, electron microscopy, dynamic light scattering, optical spectroscopy, and amyloid-specific dyes. IB-18, in comparison with IB-30, has a higher solubility in denaturants, suggesting a difference between IBs in the conformation of the associated polypeptide chains. The spectroscopic analysis revealed that rOmpF-His IBs have a high content of secondary structure with a tertiary-structure elements, including a native-like conformation, the proportion of which in IB-18 is higher than in IB-30. Solubilization of the porin from IBs is accompanied by a modification of its secondary structure. The studied IBs also contain amyloid-like structures. The results obtained in this study expand our knowledge of the structural organization of IBs formed by proteins of different structural classes and also have a contribution into the new approaches development of producing functionally active recombinant membrane proteins.
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Affiliation(s)
- Tamara F Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Svetlana I Bakholdina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia.
| | - Valentina A Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgeniy V Sidorin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Natalya Yu Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Olga D Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Valery L Shnyrov
- Departamento de Bioquimica y Biologia Molecular, Universidad de Salamanca, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Anna M Stenkova
- Far Eastern Federal University School of Biomedicine, Russky Island Ajax Bay 10, 690922 Vladivostok, Russia
| | - Vyacheslav I Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgenia P Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
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29
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Engelhardt PM, Rueda SF, Drexelius M, Neudörfl JM, Lauster D, Hackenberger CPR, Kühne R, Neundorf I, Schmalz HG. Synthetic α-Helical Peptides as Potential Inhibitors of the ACE2 SARS-CoV-2 Interaction. Chembiochem 2022; 23:e202200372. [PMID: 35785462 PMCID: PMC9350387 DOI: 10.1002/cbic.202200372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/04/2022] [Indexed: 11/11/2022]
Abstract
During viral cell entry, the spike protein of SARS‐CoV‐2 binds to the α1‐helix motif of human angiotensin‐converting enzyme 2 (ACE2). Thus, alpha‐helical peptides mimicking this motif may serve as inhibitors of viral cell entry. For this purpose, we employed the rigidified diproline‐derived module ProM‐5 to induce α‐helicity in short peptide sequences inspired by the ACE2 α1‐helix. Starting with Ac‐QAKTFLDKFNHEAEDLFYQ‐NH2 as a relevant section of α1, a series of peptides, N‐capped with either Ac‐βHAsp‐[ProM‐5] or Ac‐βHAsp‐PP, were prepared and their α‐helicities were investigated. While ProM‐5 clearly showed a pronounced effect, an even increased degree of helicity (up to 63 %) was observed in sequences in which non‐binding amino acids were replaced by alanine. The binding affinities of the peptides towards the spike protein, as determined by means of microscale thermophoresis (MST), revealed only a subtle influence of the α‐helical content and, noteworthy, led to the identification of an Ac‐βHAsp‐PP‐capped peptide displaying a very strong binding affinity (KD=62 nM).
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Affiliation(s)
| | - Sebastián Florez Rueda
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, chemical biology, GERMANY
| | - Marco Drexelius
- University of Cologne: Universitat zu Koln, Chemistry, GERMANY
| | | | - Daniel Lauster
- Freie Universitat Berlin Fachbereich Biologie Chemie Pharmazie, biochemistry and chemistry, GERMANY
| | - Christian P R Hackenberger
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, chemical biology, GERMANY
| | - Ronald Kühne
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, drug discovery, GERMANY
| | - Ines Neundorf
- University of Cologne: Universitat zu Koln, chemistry and biochemistry, GERMANY
| | - Hans-Günther Schmalz
- Universitat zu Koln, Department für Chemie, Greinstrasse 4, 50939, Köln, GERMANY
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Alshammari SO, Aldakhil T, Alshammari QA, Salehi D, Ahmed A. Cytotoxic activity of non-specific lipid transfer protein (nsLTP1) from Ajwain (Trachyspermum ammi) seeds. BMC Complement Med Ther 2022; 22:135. [PMID: 35578215 DOI: 10.1186/s12906-022-03616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Background Trachyspermum ammi, commonly known as Ajwain, is a member of the Apiaceae family. It is a therapeutic herbal spice with diverse pharmacological properties, used in traditional medicine for various ailments. However, all previous studies were conducted using small molecule extracts, leaving the protein’s bioactivity undiscovered. Aim The current study aimed to demonstrate the cytotoxic activity of Ajwain non-specific lipid transfer protein (nsLTP1) in normal breast (MCF10A), breast cancer (MCF-7), and pancreatic cancer (AsPC-1) cell lines. Also, to evaluate its structural stability in human serum as well as at high temperature conditions. Methods The cytotoxic activity of Ajwain nsLTP1 was evaluated in MCF-7 and AsPC-1 cell lines using MTT assay. Annexin V-FITC and PI staining were used to detect the early apoptotic and late apoptotic cells. The role of nsLTP1 in inducing apoptosis was further studied by quantifying Bcl-2, Bax, Caspase-3, Survivin, EGFR, and VEGF genes expression using RT-PCR. CD spectroscopy analyzed the nsLTP1 conformational changes after thermal treatment for structure stability determination. The RP-HPLC was used to analyze the nsLTP1 degradation rate in human serum at different time intervals incubated at 37 °C. Results Ajwain nsLTP1 showed a potent cytotoxic effect in MCF-7 and AsPC-1. The IC50 value obtained in MCF-7 was 8.21 μM, while for AsPC-1 4.17 μM. The effect of nsLTP1 on stimulating apoptosis revealed that the proportions of apoptotic cells in both cell lines were relatively increased depending on the concentration. The apoptotic cells percentage at 20 μM was in MCF-7 71% (***P < 0.001) and AsPC-1 88% (***P < 0.001). These results indicate that nsLTP1 might efficaciously induce apoptosis in multiple types of cancerous cells. Genes expression in MCF-7 and AsPC-1 showed significant upregulation in Bax and Caspase-3 and downregulation in Bcl-2, Survivin, EGFR, and VEGF protein. The CD analysis of nsLTP1 showed a significant thermostable property. In serum, nsLTP1 showed a slow degradation rate, indicating high stability with a half-life of ~ 8.4 h. Conclusion Our results revealed the potential anticancer activity of Ajwain nsLTP1 and its mechanism in inducing apoptosis. It further exhibited thermostable properties at high temperatures and in human serum, which suggested this protein as a promising anticancer agent. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-022-03616-y.
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Infanta S AKT, Durairaju N, Raja S, Murugesan T, Dhanapal AR, Natarajan K, Balakrishnan A, Vedagiri H, Muthusamy P, Jayaraman A. Pharmacological assessment of Ru(II) complex with GidA protein- A novel topoisomerase II inhibitor towards cancer therapeutics. J Biomol Struct Dyn 2022; 41:4143-4153. [PMID: 35514135 DOI: 10.1080/07391102.2022.2064332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The interactions of ruthenium(II) complex with Glucose inhibited division protein A (GidA protein) was studied through various spectroscopic techniques with the ultimate goal of preparing adducts with good selectivity for cancer cells. In all the cases, formation of a tight metal-protein conjugate was observed. The influence of pH, reducing agents and chelators on the formation of adduct was analysed by UV- visible spectroscopy. While there was no effect on the addition of sodium ascorbate, some alterations on some selected bands were seen on the UV-visible spectra on the addition of EDTA. The adduct was stable in the pH range of 5-8. Addition of ruthenium(II) complex effectively quenched the intrinsic fluorescence of GidA and it occurred through static quenching. The effect of ruthenium(II) complex on the conformation of GidA has been examined by analyzing CD spectrum. Though, there was some conformational changes observed in the presence of ruthenium(II) complex, α- helix in the secondary structure of GidA retained its identity. Molecular docking of ruthenium(II) complex with GidA also indicated that GidA docks through hydrophobic interaction. The stable semisynthetic complex (ruthenium(II) complex with GidA) was checked for topoisomerase II inhibition. Relaxation and decatenation assay proved topoisomerase II inhibition of semisynthetic complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Antony K Teresa Infanta S
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.,Department of Biotechnology, New Prince Shri Bhavani Arts and Science College, Chennai, Tamil Nadu, India
| | - Nisshanthini Durairaju
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Senthil Raja
- Department of Chemistry, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Thandeeswaran Murugesan
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Anand Raj Dhanapal
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | | | - Ajithkumar Balakrishnan
- Molecular Genomics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Hemamalini Vedagiri
- Molecular Genomics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Palaniswamy Muthusamy
- Department of Microbiology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Angayarkanni Jayaraman
- Cancer Therapeutics Lab, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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Tian J, Jiang YX, Yu XQ, Yu SS. Rapid chiral assay of amino compounds using diethyl squarate. Spectrochim Acta A Mol Biomol Spectrosc 2022; 272:120871. [PMID: 35151169 DOI: 10.1016/j.saa.2022.120871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The versatility and importance of chiral compounds make it urgent to develop fast and efficient methods to detect the absolute configuration, enantiomeric excess(ee), and concentration of chiral compounds. In this study, we demonstrate that commercially available diethyl squarate can rapidly react with various types of chiral amino compounds and exhibit characteristic ultraviolet (UV) and circular dichroism (CD) signals. The UV and CD signals can determine the total concentration of the two enantiomers and ee value of the sample, respectively. The probe showed a broad substrate scope, applicable to 39 tested chiral amino compounds, including chiral amino acids, amino alcohols, and amines. Additionally, the probe accurately detected 10 samples of phenylalanine, phenylglycinol, and phenethylamine with the error range less than 8%, demonstrating the practicability of this method.
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Affiliation(s)
- Jun Tian
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China
| | - Yi-Xuan Jiang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China.
| | - Shan-Shan Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China.
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Trinh KH, Kadam US, Rampogu S, Cho Y, Yang KA, Kang CH, Lee KW, Lee KO, Chung WS, Hong JC. Development of novel fluorescence-based and label-free noncanonical G4-quadruplex-like DNA biosensor for facile, specific, and ultrasensitive detection of fipronil. J Hazard Mater 2022; 427:127939. [PMID: 34893377 DOI: 10.1016/j.jhazmat.2021.127939] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Fipronil is a broad-spectrum insecticide widely used in agriculture and residential areas; its indiscriminate use leads to environmental pollution and poses health hazards. Early detection of fipronil is critical to prevent the deleterious effects. However, current insecticide analysis methods such as HPLC, LC/MS, and GC/MS are incompetent; they are costly, immobile, time-consuming, laborious, and need skilled technicians. Hence, a sensitive, specific, and cheap biosensor are essential to containing the contamination. Here, we designed two novel biosensors-the first design relied on fluorescent labeling/quenching, while the second sensor focused on label-free detection using Thioflavin T displacement. Altogether, we identified four candidate aptamers, predicted secondary structures, and performed 3D molecular modeling to predict the binding pocket of fipronil in FiPA6B aptamer. Furthermore, the aptameric sensors showed high sensitivity to fipronil of sub-ppb level LOD, attributed to stringent experimental design. The biosensors displayed high specificity against other phenylpyrazole insecticides and demonstrated robust sensitivity for fipronil in real samples like cabbage and cucumber. Notably, to the best of our knowledge, this is the first demonstration of noncanonical G4-quadruplex-like aptamer binding to fipronil, verified using CD spectroscopy. Such aptasensors possess considerable potential for real-time measurements of hazardous insecticides as point-of-care technology.
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Affiliation(s)
- Kien Hong Trinh
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 12400, Vietnam
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Shailima Rampogu
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Yuhan Cho
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyung-Ae Yang
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Keun-Woo Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Woo Sik Chung
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Plant Sciences, University of Missouri, Columbia, Missouri, MO 65211, USA.
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Barreda-Huerta F, Bustos-Jaimes I, Mújica-Jiménez C, Muñoz-Clares RA. Multiple conformations in solution of the maize C 4-phosphoenolpyruvate carboxylase isozyme. Heliyon 2021; 7:e08464. [PMID: 34888425 DOI: 10.1016/j.heliyon.2021.e08464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
The photosynthetic phosphoenolpyruvate carboxylase isozyme from C4 plants (PEPC-C4) has a complex allosteric regulation, involving positive cooperativity in binding the substrate phosphoenolpyruvate as well as positive and negative allosteric effectors. Besides the proposed R- and T-states, previous kinetic results suggested functionally relevant different R-states of the maize enzyme (ZmPEPC-C4) elicited by PEP or its two kinds of activators, glucose 6-phosphate or glycine. To detect these different R-state conformations, we used as conformational probes the fluorescence of 8-anilino-1-naphthalene sulfonate (ANS), near-UV circular dichroism (CD) spectroscopy, and limited proteolysis by trypsin. Phosphoenolpyruvate and malate binding caused distinct concentration-dependent fluorescence changes of ZmPEPC-C4/ANS, suggesting that they elicited conformational states different from that of the free enzyme, while glucose 6-phosphate or glycine binding did not produce fluorescence changes. Differences were also observed in the near UV CD spectra of the enzyme, free or complexed with its substrate or allosteric effectors. Additionally, differences in the trypsin-digestion fragmentation patterns, as well as in the susceptibility of the free and complexed enzyme to digestion and digestion-provoked loss of activity, provided evidence of several ZmPEPC-C4 conformations in solution elicited by the substrate and the allosteric effectors. Using the already reported ZmPEPC-C4 crystal structures and bioinformatics methods, we predicted that the most probable trypsin-cleavage sites are located in superficial flexible regions, which seems relevant for the protein dynamics underlying the function and allosteric regulation of this enzyme. Together, our findings agree with previous kinetic results, shed light on this enzyme's complex allosteric regulation, and place ZmPEPC-C4 in the growing list of allosteric enzymes possessing an ensemble of closely related R-state conformations. PEP or malate binding produce distinct changes in ZmPEPC-C4/ANS fluorescence. Different near-UV CD spectra of the free enzyme or of the enzyme complexes were observed. PEP or effectors binding produce distinctive ZmPEPC-C4 trypsin-fragmentation patterns. Our results support several ligand-induced ZmPEPC-C4 conformational states in solution. Predicted trypsin-cleavage sites are at flexible loops, which probably participate in ZmPEPC-C4 function and regulation.
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Maračić S, Grbčić P, Shammugam S, Radić Stojković M, Pavelić K, Sedić M, Kraljević Pavelić S, Raić-Malić S. Amidine- and Amidoxime-Substituted Heterocycles: Synthesis, Antiproliferative Evaluations and DNA Binding. Molecules 2021; 26:molecules26227060. [PMID: 34834151 PMCID: PMC8625065 DOI: 10.3390/molecules26227060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
The novel 1,2,3-triazolyl-appended N- and O-heterocycles containing amidine 4–11 and amidoxime 12–22 moiety were prepared and evaluated for their antiproliferative activities in vitro. Among the series of amidine-substituted heterocycles, aromatic diamidine 5 and coumarine amidine 11 had the most potent growth-inhibitory effect on cervical carcinoma (HeLa), hepatocellular carcinoma (HepG2) and colorectal adenocarcinoma (SW620), with IC50 values in the nM range. Although compound 5 was toxic to non-tumor HFF cells, compound 11 showed certain selectivity. From the amidoxime series, quinoline amidoximes 18 and 20 showed antiproliferative effects on lung adenocarcinoma (A549), HeLa and SW620 cells emphasizing compound 20 that exhibited no cytostatic effect on normal HFF fibroblasts. Results of CD titrations and thermal melting experiments indicated that compounds 5 and 10 most likely bind inside the minor groove of AT-DNA and intercalate into AU-RNA. Compounds 6, 9 and 11 bind to AT-DNA with mixed binding mode, most probably minor groove binding accompanied with aggregate binding along the DNA backbone.
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Affiliation(s)
- Silvija Maračić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
| | - Petra Grbčić
- Department of Biotechnology, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia;
| | - Suresh Shammugam
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia;
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia;
- Correspondence: (M.R.S.); (S.R.-M.); Tel.: +385-1-4571220 (M.R.S.); +385-1-4597213 (S.R.-M.)
| | - Krešimir Pavelić
- Faculty of Medicine, Juraj Dobrila University of Pula, HR-52100 Pula, Croatia;
| | - Mirela Sedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, HR-10000 Zagreb, Croatia;
| | - Sandra Kraljević Pavelić
- Faculty of Health Studies, University of Rijeka, Ulica Viktora Cara Emina 5, HR-51000 Rijeka, Croatia;
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
- Correspondence: (M.R.S.); (S.R.-M.); Tel.: +385-1-4571220 (M.R.S.); +385-1-4597213 (S.R.-M.)
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Bulyáki É, Kun J, Molnár T, Papp A, Micsonai A, Vadászi H, Márialigeti B, Kovács AI, Gellén G, Yamaguchi K, Lin Y, So M, Józsi M, Schlosser G, Lee YH, Liliom K, Goto Y, Kardos J. Pathogenic D76N Variant of β 2-Microglobulin: Synergy of Diverse Effects in Both the Native and Amyloid States. Biology (Basel) 2021; 10:biology10111197. [PMID: 34827190 PMCID: PMC8614874 DOI: 10.3390/biology10111197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023]
Abstract
Simple Summary Elevated β2-microglobulin (β2m) serum levels cause serious complications in patients on long-term kidney dialysis by depositing in the form of amyloid fibrils in the osteoarticular system. Recently, a hereditary systemic amyloidosis was discovered, caused by a naturally occurring D76N β2m mutant exhibiting normal serum levels and a distinct, visceral deposition pattern. D76N β2m showed a structure remarkably similar to the wild-type (WT) protein, albeit with decreased thermodynamic stability and increased amyloidogenicity. Despite the extensive research, the molecular bases of the aberrant aggregation of β2m in vivo remains elusive. Here, using a variety of biophysical techniques, we investigated the role of the pathogenic D76N mutation in the amyloid formation of β2m by point mutations affecting the stabilizing ion-pairs of β2m. We found that, relative to WT β2m, the exceptional amyloidogenicity of the pathogenic D76N β2m variant is realized by the synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular matrix proteins. Understanding the underlying molecular mechanisms might help to find target points for effective treatments against diseases associated with the deleterious aggregation of proteins. Abstract β2-microglobulin (β2m), the light chain of the MHC-I complex, is associated with dialysis-related amyloidosis (DRA). Recently, a hereditary systemic amyloidosis was discovered, caused by a naturally occurring D76N β2m variant, which showed a structure remarkably similar to the wild-type (WT) protein, albeit with decreased thermodynamic stability and increased amyloidogenicity. Here, we investigated the role of the D76N mutation in the amyloid formation of β2m by point mutations affecting the Asp76-Lys41 ion-pair of WT β2m and the charge cluster on Asp38. Using a variety of biophysical techniques, we investigated the conformational stability and partial unfolding of the native state of the variants, as well as their amyloidogenic propensity and the stability of amyloid fibrils under various conditions. Furthermore, we studied the intermolecular interactions of WT and mutant proteins with various binding partners that might have in vivo relevance. We found that, relative to WT β2m, the exceptional amyloidogenicity of the pathogenic D76N β2m variant is realized by the deleterious synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules (e.g., lipids) and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular components, including extracellular matrix proteins.
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Affiliation(s)
- Éva Bulyáki
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Judit Kun
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Tamás Molnár
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Alexandra Papp
- Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (A.P.); (M.J.)
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Henrietta Vadászi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
| | - Borbála Márialigeti
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Attila István Kovács
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (T.M.); (B.M.); (A.I.K.)
| | - Gabriella Gellén
- Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (G.S.)
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; (K.Y.); (Y.G.)
| | - Yuxi Lin
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Masatomo So
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan; or
| | - Mihály Józsi
- Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (A.P.); (M.J.)
- MTA-ELTE Complement Research Group, Eötvös Loránd Research Network (ELKH), Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (G.S.)
| | - Young-Ho Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea; (Y.L.); (Y.-H.L.)
- Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University (CNU), Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute (KBRI), Daegu 41068, Korea
| | - Károly Liliom
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; (K.Y.); (Y.G.)
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan; or
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (É.B.); (J.K.); (A.M.); (H.V.)
- Correspondence:
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Nowak-Karnowska J, Głuszyńska A, Kosman J, Neunert G, Dembska A. Interaction of 9-Methoxyluminarine with Different G-Quadruplex Topologies: Fluorescence and Circular Dichroism Studies. Int J Mol Sci 2021; 22:10399. [PMID: 34638738 DOI: 10.3390/ijms221910399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
The interactions of G-quadruplexes of different topologies with highly fluorescent 9-methoxyluminarine ligand 9-MeLM were investigated by fluorescence and circular dichroism spectroscopy. The results showed that 9-methoxyluminarine was able to interact and did not destabilize any investigated molecular targets. The studied compound was selectively quenched by parallel c-MYC G-quadruplex DNA, whereas hybrid and antiparallel G4 topology caused only a negligible decrease in the fluorescence of the ligand. A high decrease of fluorescence of the ligand after binding with c-MYC G-quadruplex suggests that this molecule can be used as a selective probe for parallel G-quadruplexes.
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Vijeesh V, Jisha N, Vysakh A, Latha MS. Interaction of eugenol with xanthine oxidase: Multi spectroscopic and in silico modelling approach. Spectrochim Acta A Mol Biomol Spectrosc 2021; 258:119843. [PMID: 33933941 DOI: 10.1016/j.saa.2021.119843] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/04/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Eugenol, a major component in clove has various biological activities. The current study focused to the binding potential of eugenol with Xanthine oxidase (XO) were evaluated using multi spectroscopic techniques and in silico docking studies. Xanthine oxidase, a superoxide generating enzyme, catalyses hypoxanthine and xanthine to uric acid. An excessive uric acid and superoxide anion radical in our body causes many serious clinical complications. The activity and the structural alterations can be a significant method to reduce this kind of risk factors. The results obtained from the fluorescence titration exhibited the interactions initiated by a static quenching mechanism. The ultraviolet (UV), fourier-transform infrared (FTIR), circular dichroism (CD) spectroscopic analysis of eugenol bind with XO indicated the secondary structural alteration in XO. Docking studies showed molecular level interaction of eugenol with the amino acid residues of Thr 1010, Phe 914, Phe 1009, Leu 1014, Phe 1009, Val 1011, Arg 880, Ala 1078, Glu 802, Leu 648and Leu 873 which residing at the catalytic active site of the XO. These results inferred that the eugenol can interact with XO in a remarkable manner and these findings provide a supporting data for the XO inhibition studies to propose a new lead compound.
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Affiliation(s)
- V Vijeesh
- School of Biosciences, Mahatma Gandhi University, Priyadarshini Hills, Kottayam, Kerala, India
| | - Ninan Jisha
- School of Biosciences, Mahatma Gandhi University, Priyadarshini Hills, Kottayam, Kerala, India
| | - A Vysakh
- School of Biosciences, Mahatma Gandhi University, Priyadarshini Hills, Kottayam, Kerala, India
| | - M S Latha
- School of Biosciences, Mahatma Gandhi University, Priyadarshini Hills, Kottayam, Kerala, India.
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Kejnovská I, Stadlbauer P, Trantírek L, Renčiuk D, Gajarský M, Krafčík D, Palacký J, Bednářová K, Šponer J, Mergny JL, Vorlíčková M. G-Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly. Chemistry 2021; 27:12115-12125. [PMID: 34145655 DOI: 10.1002/chem.202100895] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 02/05/2023]
Abstract
Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that are frequently found in genomes. The stability of G4s depends, among other factors, on the number of G-tetrads. Three- or four-tetrad G4s and antiparallel two-tetrad G4s have been characterized experimentally; however, the existence of an intramolecular (i. e., not dimeric or multimeric) two-tetrad parallel-stranded DNA G4 has never been experimentally observed. Many sequences compatible with two-tetrad G4 can be found in important genomic regions, such as promoters, for which parallel G4s predominate. Using experimental and theoretical approaches, the propensity of the model sequence AATGGGTGGGTTTGGGTGGGTAA to form an intramolecular parallel-stranded G4 upon increasing the number of GGG-to-GG substitutions has been studied. Deletion of a single G leads to the formation of intramolecular G4s with a stacked G-triad, whose topology depends on the location of the deletion. Removal of another guanine from another G-tract leads to di- or multimeric G4s. Further deletions mostly prevent the formation of any stable G4. Thus, a solitary two-tetrad parallel DNA G4 is not thermodynamically stable and requires additional interactions through capping residues. However, transiently populated metastable two-tetrad species can associate to form stable dimers, the dynamic formation of which might play additional delicate roles in gene regulation. These findings provide essential information for bioinformatics studies searching for potential G4s in genomes.
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Affiliation(s)
- Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Martin Gajarský
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
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Kopp N, Civenni G, Marson D, Laurini E, Pricl S, Catapano CV, Humpf HU, Almansa C, Nieto FR, Schepmann D, Wünsch B. Chemoenzymatic synthesis of 2,6-disubstituted tetrahydropyrans with high σ 1 receptor affinity, antitumor and analgesic activity. Eur J Med Chem 2021; 219:113443. [PMID: 33901806 DOI: 10.1016/j.ejmech.2021.113443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
1,3-Dioxanes 1 and cyclohexanes 2 bearing a phenyl ring and an aminoethyl moiety in 1,3-relationship to each other represent highly potent σ1 receptor antagonists. In order to increase the chemical stability of the acetalic 1,3-dioxanes 1 and the polarity of the cyclohexanes 2, tetrahydropyran derivatives 3 equipped with the same substituents were designed, synthesized and pharmacologically evaluated. The key step of the synthesis was a lipase-catalyzed enantioselective acetylation of the alcohol (R)-5 leading finally to enantiomerically pure test compounds 3a-g. With respect to σ1 receptor affinity and selectivity over a broad range of related (σ2, PCP binding site) and further targets, the enantiomeric benzylamines 3a and cyclohexylmethylamines 3b represent the most promising drug candidates of this series. However, the eudismic ratio for σ1 binding is only in the range of 2.5-3.3. Classical molecular dynamics (MD) simulations confirmed the same binding pose for both the tetrahydropyran 3 and cyclohexane derivatives 2 at the σ1 receptor, according to which: i) the protonated amino moiety of (2S,6R)-3a engages the same key polar interactions with Glu172 (ionic) and Phe107 (π-cation), ii) the lipophilic parts of (2S,6R)-3a are hosted in three hydrophobic regions of the σ1 receptor, and iii) the O-atom of the tetrahydropyran derivatives 3 does not show a relevant interaction with the σ1 receptor. Further in silico evidences obtained by the application of free energy perturbation and steered MD techniques fully supported the experimentally observed difference in receptor/ligand affinities. Tetrahydropyrans 3 require a lower dissociative force peak than cyclohexane analogs 2. Enantiomeric benzylamines 3a and cyclohexylmethylamines 3b were able to inhibit the growth of the androgen negative human prostate cancer cell line DU145. The cyclohexylmethylamine (2S,6R)-3b showed the highest σ1 affinity (Ki(σ1) = 0.95 nM) and the highest analgesic activity in vivo (67%).
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Affiliation(s)
- Nicole Kopp
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
| | - Gianluca Civenni
- Institute of Oncology Research, Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Carlo V Catapano
- Institute of Oncology Research, Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Hans-Ulrich Humpf
- Institut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149, Münster, Germany
| | - Carmen Almansa
- Esteve Pharmaceuticals S.A., Baldiri Reixach 4-8, 08028, Barcelona, Spain
| | - Francisco Rafael Nieto
- Department of Pharmacology and Neurosciences Institute (Biomedical Research Center), University of Granada and Biosanitary Research Institute, 18010, Granada, Spain
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany; GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Germany.
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41
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Murvai N, Kalmar L, Szabo B, Schad E, Micsonai A, Kardos J, Buday L, Han KH, Tompa P, Tantos A. Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14. Int J Mol Sci 2021; 22:6190. [PMID: 34201246 PMCID: PMC8230022 DOI: 10.3390/ijms22126190] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/04/2022] Open
Abstract
Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana's Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.
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Grants
- G.0029.12 Research Foundation Flanders
- 2010-88343 Korea Research Council of Fundamental Science and Technology
- NTM2231712 National Research Council of Science and Technology
- K124670 National Research, Development and Innovation Office, Hungary
- K131702 National Research, Development and Innovation Office, Hungary
- K125340 National Research, Development and Innovation Office, Hungary
- K120391 National Research, Development and Innovation Office, Hungary
- KH125597 National Research, Development and Innovation Office, Hungary
- PD135510 National Research, Development and Innovation Office, Hungary
- Bolyai János Scholarship Hungarian Academy of Sciences
- 20171582 SOLEIL Synchrotron, France
- 20180805 SOLEIL Synchrotron, France
- 20181890 SOLEIL Synchrotron, France
- Lendület Grant Hungarian Academy of Sciences
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Affiliation(s)
- Nikoletta Murvai
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Lajos Kalmar
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Beata Szabo
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Eva Schad
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - László Buday
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Kyou-Hoon Han
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Gene Editing Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Peter Tompa
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Agnes Tantos
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
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42
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Robustelli J, Baumgart T. Membrane partitioning and lipid selectivity of the N-terminal amphipathic H0 helices of endophilin isoforms. Biochim Biophys Acta Biomembr 2021; 1863:183660. [PMID: 34090873 DOI: 10.1016/j.bbamem.2021.183660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 11/26/2022]
Abstract
Endophilin is an N-BAR protein, which is characterized by a crescent-shaped BAR domain and an amphipathic helix that contributes to the membrane binding of these proteins. The exact function of that H0 helix has been a topic of debate. In mammals, there are five different endophilin isoforms, grouped into A (three members) and B (two members) subclasses, which have been described to differ in their subcellular localization and function. We asked to what extent molecular properties of the H0 helices of these members affect their membrane targeting behavior. We found that all H0 helices of the endophilin isoforms display a two-state equilibrium between disordered and α-helical states in which the helical secondary structure can be stabilized through trifluoroethanol. The helicities in high TFE were strikingly different among the H0 peptides. We investigated H0-membrane partitioning by the monitoring of secondary structure changes via CD spectroscopy. We found that the presence of anionic phospholipids is critical for all H0 helices partitioning into membranes. Membrane partitioning is found to be sensitive to variations in membrane complexity. Overall, the H0 B subfamily displays stronger membrane partitioning than the H0 A subfamily. The H0 A peptide-membrane binding occurs predominantly through electrostatic interactions. Variation among the H0 A subfamily may be attributed to slight alterations in the amino acid sequence. Meanwhile, the H0 B subfamily displays greater specificity for certain membrane compositions, and this may link H0 B peptide binding to endophilin B's cellular function.
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Affiliation(s)
- Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States.
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43
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. Eur Biophys J 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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Balcerowicz M, Di Antonio M, Chung BYW. Monitoring Real-time Temperature Dynamics of a Short RNA Hairpin Using Förster Resonance Energy Transfer and Circular Dichroism. Bio Protoc 2021; 11:e3950. [PMID: 33855112 DOI: 10.21769/bioprotoc.3950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 11/02/2022] Open
Abstract
RNA secondary structures are highly dynamic and subject to prompt changes in response to the environment. Temperature in particular has a strong impact on RNA structural conformation, and temperature-sensitive RNA hairpin structures have been exploited by multiple organisms to modify the rate of translation in response to temperature changes. Observing RNA structural changes in real-time over a range of temperatures is therefore highly desirable. A variety of approaches exists that probe RNA secondary structures, but many of these either require large amount and/or extensive processing of the RNA or cannot be applied under physiological conditions, rendering the observation of structural dynamics over a range of temperatures difficult. Here, we describe the use of a dually fluorescently labelled RNA oligonucleotide (containing the predicted hairpin structure) that can be used to monitor subtle RNA-structural dynamics by Förster Resonance Energy Transfer (FRET) at different temperatures with RNA concentration as low as 200 nM. FRET efficiency varies as a function of the fluorophores' distance; high efficiency can thus be correlated to a stable hairpin structure, whilst a reduction in FRET efficiency reflects a partial opening of the hairpin or a destabilisation of this structure. The same RNA sequence can also be used for Circular Dichroism spectroscopy to observe global changes of RNA secondary structure at a given temperature. The combination of these approaches allowed us to monitor RNA structural dynamics over a range of temperatures in real-time and correlate structural changes to plant biology phenotypes. Graphic abstract: Monitoring temperature-dependent RNA structural dynamics using Förster Resonance Energy Transfer (FRET).
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Affiliation(s)
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Science Research Hub, London, UK.,The Institute of Chemical Biology (ICB), Molecular Science Research Hub, London, UK
| | - Betty Y W Chung
- Department of Pathology, University of Cambridge, Cambridge, UK
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45
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Lu W, Gong L, Su C, Wang Q, Ling Q, Wang P, Qi D, Bian Y. Intermolecular Chirality Modulation of Binaphthalene-Bridged Bisporphyrins With Chiral Diamines. Front Chem 2021; 8:611257. [PMID: 33659235 PMCID: PMC7919525 DOI: 10.3389/fchem.2020.611257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
A new pair of 2,2ʹ-diamino-1,1ʹ-binaphthyl linked porphyrin dimers, (R)-/(S)-H, were synthesized to study their supramolecular interactions with a pair of chiral diamines ((R)-/(S)-PPDA) by using UV-Vis absorption, fluorescence and NMR titrations. The spectroscopic titrations indicated that sandwich-type 1:1 complexes were formed at low guest concentration and then transformed to 1:2 open complexes at high guest concentration. The supramolecular interactions afforded sensitive circular dichroism responses, and the CD signs of the 1:1 complexes are decided by the stereostructure of chiral diamine guests. Moreover, due to the shortened linking units, (R)-/(S)-H show more sensitive and predicable CD response than the previously reported hosts (R)-/(S)-H1 and this can be reasonably explained by DFT molecular modeling. The present results suggest (R)-/(S)-H are promising for chiral optical sensing.
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Affiliation(s)
- Wenxin Lu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China.,Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing, China
| | - Lei Gong
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing, China
| | - Chaorui Su
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing, China
| | - Qibao Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Qing Ling
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Peng Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Dongdong Qi
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing, China
| | - Yongzhong Bian
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing, China
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Kopp N, Holtschulte C, Börgel F, Lehmkuhl K, Friedland K, Civenni G, Laurini E, Catapano CV, Pricl S, Humpf HU, Schepmann D, Wünsch B. Novel σ 1 antagonists designed for tumor therapy: Structure - activity relationships of aminoethyl substituted cyclohexanes. Eur J Med Chem 2021; 210:112950. [PMID: 33148494 DOI: 10.1016/j.ejmech.2020.112950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/19/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
Depending on the substitution pattern and stereochemistry, 1,3-dioxanes 1 with an aminoethyl moiety in 4-position represent potent σ1 receptor antagonists. In order to increase the stability, a cyclohexane ring first replaced the acetalic 1, 3-dioxane ring of 1. A large set of aminoethyl substituted cyclohexane derivatives was prepared in a six-step synthesis. All enantiomers and diastereomers were separated by chiral HPLC at the stage of the primary alcohol 7, and their absolute configuration was determined by CD spectroscopy. Neither the relative nor the absolute configuration had a large impact on the σ1 affinity. The highest σ1 affinity was found for cis-configured benzylamines (1R,3S)-11 (Ki = 0.61 nM) and (1S,3R)-11 (Ki = 1.3 nM). Molecular dynamics simulations showed that binding of (1R,3S)-11 at the σ1 receptor is stabilized by the typical polar interaction of the protonated amino moiety with the carboxy group of E172 which is optimally oriented by an H-bond interaction with Y103. The lipophilic interaction of I124 with the N-substituent also contributes to the high σ1 affinity of the benzylamines. The antagonistic activity was determined in a Ca2+ influx assay in retinal ganglion cells. The enantiomeric cis-configured benzylamines (1R,3S)-11 and (1S,3R)-11 were able to inhibit the growth of DU145 cells, a highly aggressive human prostate tumor cell line. Moreover, cis-11 could also inhibit the growth of further human tumor cells expressing σ1 receptors. The experimentally determined logD7.4 value of 3.13 for (1R,3S)-11 is in a promising range regarding membrane penetration. After incubation with mouse liver microsomes and NADPH for 90 min, 43% of the parent (1R,3S)-11 remained unchanged, indicating intermediate metabolic stability. Altogether, nine metabolites including one glutathione adduct were detected by means of LC-MS analysis.
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Affiliation(s)
- Nicole Kopp
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Catharina Holtschulte
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Frederik Börgel
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Kirstin Lehmkuhl
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Kristina Friedland
- Pharmacology and Toxicology, Pharmacy and Biochemistry, Johannes Gutenberg University, Staudingerweg 5, 55128 Mainz, Germany
| | - Gianluca Civenni
- Institute of Oncology Research, Universita Della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Carlo V Catapano
- Institute of Oncology Research, Universita Della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Hans-Ulrich Humpf
- Institut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, Germany
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), Westfälische Wilhelms-Universität Münster, Germany.
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Koyiloth M, Gummadi SN. Cholesterol interaction attenuates scramblase activity of SCRM-1 in the artificial membrane. Biochim Biophys Acta Biomembr 2021; 1863:183548. [PMID: 33417966 DOI: 10.1016/j.bbamem.2020.183548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/09/2023]
Abstract
Phospholipid (PL) scramblases are single-pass transmembrane protein mediating bidirectional PL translocation. Previously in silico analysis of human PL scramblases, predicted the presence of an uncharacterized cholesterol-binding domain spanning partly in the transmembrane helix as well as in the adjacent extracellular coil. This domain was found to be universally conserved in diverse organisms like Caenorhabditis elegans. In this study, we investigated the saturable cholesterol-binding domain of SCRM-1 using fluorescence sterol binding assay, Stern-Volmer quenching, Förster resonance energy transfer, and CD spectroscopy. We observed high-affinity interaction between cholesterol and SCRM-1. Our results support a previous report, which showed that the cholesterol ordering effect reduced the scramblase activity of hPLSCR1. Considering the presence of a high-affinity binding sequence, we propose that the reduction in activity could partly be due to the cholesterol binding. To validate this, we generated a C-terminal helix (CTH) deletion construct (∆CTH SCRM-1) and a point mutation in the putative cholesterol-binding domain I273D SCRM-1. Deletion construct greatly reduced cholesterol affinity along with loss of scramblase activity. In contrast to this, I273D SCRM-1 retained scrambling activity in proteoliposomes containing ~30 mol% cholesterol but lost sterol binding ability. These results suggest that C-terminal helix is crucial for membrane insertion and in the lipid bilayer the scrambling activity of SCRM-1 is modulated through its interaction with cholesterol.
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D’Aria F, Pagano B, Petraccone L, Giancola C. KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study. Int J Mol Sci 2021; 22:ijms22010448. [PMID: 33466280 PMCID: PMC7795837 DOI: 10.3390/ijms22010448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/23/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.
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Affiliation(s)
- Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy;
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
- Correspondence:
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Shamim A, Razzaq M, Kim KK. MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif. Int J Mol Sci 2020; 22:E61. [PMID: 33374624 DOI: 10.3390/ijms22010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/23/2022] Open
Abstract
I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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