1
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Todorov P, Georgieva S, Trapella C, Chakarov K, Tchekalarova J, Pechlivanova D, Cheshmedzhieva D, Fantinati A, Illuminati D. Synthesis, characterization, and biological study of new synthetic opioid hemorphin-4 peptides containing sterically restricted nonnatural amino acids. Arch Pharm (Weinheim) 2024; 357:e2400052. [PMID: 38578075 DOI: 10.1002/ardp.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/25/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Some new hemorphin-4 analogs with structures of Xxx-Pro-Trp-Thr-NH2 and Tyr-Yyy-Trp-Thr-NH2, where Xxx is 2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid or 2-amino-3-(4-dibenzylamino-2,6-dimethylphenyl)propanoic acid, and Yyy is (2S,4S)-4-amino-pyrrolidine-2-carboxylic acid, were synthesized and characterized by electrochemical and spectral analyses. In vivo anticonvulsant and antinociceptive activities of peptide derivatives were studied after intracerebroventricular injection in mice. The therapeutic effects of the modified peptides on seizures and pain in mice were evaluated to provide valuable insights into the potential applications of the novel compounds. Electrochemical characterization showed that the compounds behave as weak protolytes and that they are in a soluble, stable molecular form at physiological pH values. The antioxidant activity of the peptides was evaluated with voltammetric analyses, which were confirmed by applying the 2,2-Diphenyl-1-picrylhydrazyl method. The compounds showed satisfactory results regarding their structural stability, reaching the desired centers for the manifestation of biological activity without hydrolysis processes at 37°C and physiological pH. Dm-H4 and H4-P1 exhibited 100% and 83% potency to suppress the psychomotor seizures in the 6-Hz test compared to 67% activity of H4. Notably, only the H4-P1 had efficacy in blocking the tonic component in the maximal electroshock test with a potency comparable to H4. All investigated peptides containing unnatural conformationally restricted amino acids showed antinociceptive effects. The analogs Db-H4 and H4-P1 showed the most pronounced and long-lasting effect in both experimental models of pain induced by thermal and chemical stimuli. Dm-H4 produced a dose-dependent thermal antinociception and H4-P2 inhibited only formalin-induced pain behavior.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Claudio Trapella
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Kalin Chakarov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Jana Tchekalarova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Daniela Pechlivanova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Faculty of Medicine, Sofia University "St. Kliment Ohridski" 1, Sofia, Bulgaria
| | - Diana Cheshmedzhieva
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Anna Fantinati
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
| | - Davide Illuminati
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
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2
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Brahma D, Sarkar T, Kaushik R, Sarangi AN, Gupta AN. Structural rearrangement of elastin under oxidative stress. Colloids Surf B Biointerfaces 2024; 233:113663. [PMID: 38008014 DOI: 10.1016/j.colsurfb.2023.113663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Reactive oxygen species (ROS) are key elements in several physiological processes. A high level of ROS leads to oxidative stress that damages biomolecules and is linked to many diseases like type-2 diabetes, cancer, inflammation, and many more. Here, our in-vitro study aimed to gauge the effect of ROS on the structural rearrangement of elastin through metal-catalyzed oxidation (MCO) at physiological temperature through laser light scattering, UV-vis, FTIR, and FESEM imaging. Light scattering data show a decrease in the hydrodynamic radius of elastin upon oxidation for the first hour. The rate of size reduction of ROS-treated elastin and the rate for self-assembly of bare elastin in the first two hours is found to be almost the same. However, the rate of association of ROS-treated is one order slower than the bare elastin after one hour. UV-vis absorption shows a blue shift accompanied by increased absorption, followed by a redshift and broadening of peak. FTIR data reveal changes in the secondary structures for both bare and oxidized elastin with time. While bare elastin coacervation increases unordered structure, the corresponding case of oxidized elastin saw a rise in β-sheet. FESEM images show the morphological changes occurring with time. Thus, we conclude that oxidative stress leads to structural rearrangement of the protein through interaction with the polar and hydrophobic domains, followed by aggregation. This study might be helpful for therapeutics focusing on preventing elastin degradation against aging.
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Affiliation(s)
- Debdip Brahma
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Tamal Sarkar
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Rupal Kaushik
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Akshay Narayan Sarangi
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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3
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Khosroshahi ME, Patel Y. Reflective FT-NIR and SERS studies of HER-II breast cancer biomarker using plasmonic-active nanostructured thin film immobilized oriented antibody. JOURNAL OF BIOPHOTONICS 2023; 16:e202200252. [PMID: 36177970 DOI: 10.1002/jbio.202200252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
We describe the fabrication of plasmonic-active nanostructured thin film substrate as a label-free surface-enhanced Raman scattering (SERS)-based biosensor immobilized covalently with monoclonal HER-II antibody (mAb) to detect overexpressed HER-II as a biomarker in breast cancer serum (BCS). Oriented conjugation of mAb via hydrazone linkage to provide higher mAb accessibility was characterized by UV-vis and reflective Fourier transform near-infrared (FT-NIR) spectroscopic techniques. The interaction of BCS with mAb was studied by FT-NIR and nonresonant SERS at 637 nm. The results showed detection of glycoprotein content at different laser powers including a rise in amino acid and glycan content with varying results at higher power. With nonresonant SERS we observed nonlinear behavior of peak intensity. Analysis of variance was implemented to determine the effect of laser power which was found not to be a contributing factor. However, at the nanoscale, factors including the heating effect and aggregation of molecules can contribute to the nonlinearity of peak intensity.
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Affiliation(s)
- Mohammad E Khosroshahi
- Nanobiophotonics and Biomedical Research Laboratory, M.I.S. Electronics Inc., Richmond Hill, Ontario, Canada
- Institute for Advanced Non-Destructive & Diagnostic Technologies (IANDIT), University of Toronto, Toronto, Ontario, Canada
| | - Yesha Patel
- Nanobiophotonics and Biomedical Research Laboratory, M.I.S. Electronics Inc., Richmond Hill, Ontario, Canada
- Department of Biochemistry, University of Waterloo, Waterloo, Ontario, Canada
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4
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Ditta SA, Yaqub A, Tanvir F, Rashid M, Ullah R, Zubair M, Ali S, Anjum KM. Gold nanoparticles capped with L-glycine, L-cystine, and L-tyrosine: toxicity profiling and antioxidant potential. JOURNAL OF MATERIALS SCIENCE 2023; 58:2814-2837. [PMID: 36743265 PMCID: PMC9888356 DOI: 10.1007/s10853-023-08209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Biomolecules-based surface modifications of nanomaterials may yield effective and biocompatible nanoconjugates. This study was designed to evaluate gold nanoconjugates (AuNCs) for their altered antioxidant potential. Gold nanoparticles (AuNPs) and their conjugates gave SPR peaks in the ranges of 512-525 nm, with red or blueshift for different conjugates. Cys-AuNCs demonstrated enhanced (p < 0.05) and Gly-AuNCs (p > 0.05) displayed reduced DPPH activity. Gly-AuNCs and Tyr-AuNCs displayed enhanced ferric-reducing power and hydrogen peroxide scavenging activity, respectively. Cadmium-intoxicated mice were exposed to gold nanomaterials, and the level of various endogenous parameters, i.e., CAT, GST, SOD, GSH, and MTs, was evaluated. GSH and MTs in liver tissues of the cadmium-exposed group (G2) were elevated (p < 0.05), while other groups showed nonsignificance deviations than the control group. It is concluded that these nanoconjugates might provide effective nanomaterials for biomedical applications. However, more detailed studies for their safety profiling are needed before their practical applications.
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Affiliation(s)
- Sarwar Allah Ditta
- Department of Zoology, Government College University, Lahore, 54000 Pakistan
| | - Atif Yaqub
- Department of Zoology, Government College University, Lahore, 54000 Pakistan
| | - Fouzia Tanvir
- Department of Zoology, University of Okara, Okara, 56300 Pakistan
| | - Muhammad Rashid
- Department of Zoology, Government College University, Lahore, 54000 Pakistan
| | - Rehan Ullah
- Department of Zoology, Government College University, Lahore, 54000 Pakistan
| | - Muhammad Zubair
- Department of Wildlife and Ecology, The University of Veterinary and Animal Sciences, Lahore, 54000 Pakistan
| | - Shaista Ali
- Department of Chemistry, Government College University, Lahore, 54000 Pakistan
| | - Khalid Mahmood Anjum
- Department of Wildlife and Ecology, The University of Veterinary and Animal Sciences, Lahore, 54000 Pakistan
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Smith E, Condict L, Ashton J, Kasapis S. Molecular interactions between soybean glycinin (11S) and genistein using spectroscopic and in silico analyses. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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6
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Todorov P, Georgieva S, Staneva D, Peneva P, Grozdanov P, Nikolova I, Vasileva-Tonkova E, Grabchev I. Study of Novel Peptides for Antimicrobial Protection in Solution and on Cotton Fabric. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154770. [PMID: 35897948 PMCID: PMC9332204 DOI: 10.3390/molecules27154770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
Some new N- and C-modified biomolecular peptide analogues of both VV-hemorphin-5 and VV-hemorphin-7 with varied amino acids (Cys, Glu, His), 1-adamantanecarboxylic acid, and niacin (nicotinic acid) were synthesized by solid-phase peptide synthesis-Fmoc (9-fluorenylmethoxy-carbonyl) chemistry and were characterized in water solutions with different pH using spectroscopic and electrochemical techniques. Basic physicochemical properties related to the elucidation of the peptide structure at physiological pH have been also studied. The results showed that the interaction of peptide compounds with light and electricity preserves the structural and conformational integrity of the compounds in the solutions. Moreover, textile cotton fibers were modified with the new compounds and the binding of the peptides to the surface of the material was proved by FTIR and SEM analysis. Washing the material with an alkaline soap solution did not show a violation of the modified structure of the cotton. Antiviral activity against the human respiratory syncytial virus (HRSV-S2) and human adenovirus serotype 5 (HAdV-5), the antimicrobial activity against B. cereus and P. aeruginosa used as model bacterial strains and cytotoxic effect of the peptide derivatives and modified cotton textile material has been evaluated. Antimicrobial tests showed promising activity of the newly synthesized compounds against the used Gram-positive and Gram-negative bacteria. The compounds C-V, H-V, AC-V, and AH-V were found slightly more active than NH7C and NCH7. The activity has been retained after the deposition of the compounds on cotton fibers.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
- Correspondence: ; Tel.: +359-2-8163423
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Desislava Staneva
- Department of Textile and Leathers, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Petia Peneva
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Petar Grozdanov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.G.); (I.N.); (E.V.-T.)
| | - Ivanka Nikolova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.G.); (I.N.); (E.V.-T.)
| | - Evgenia Vasileva-Tonkova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.G.); (I.N.); (E.V.-T.)
| | - Ivo Grabchev
- Faculty of Medicine, Sofia University “St. Kl. Ohridski”, 1407 Sofia, Bulgaria;
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Gülfen M, Özdemir A. Monitoring Cu(II)-insulin and Mn(II)-insulin complexes using potentiometric, chromatographic, UV–vis absorption and fluorescence emission spectroscopic techniques. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Gómez SA, Rojas‐Valencia N, Gómez S, Cappelli C, Restrepo A. The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Chembiochem 2022; 23:e202100393. [PMID: 34529328 PMCID: PMC8652971 DOI: 10.1002/cbic.202100393] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS-COV-2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (α or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (β or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (γ or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (ζ, or P.2 or 20B/S484K, also first reported in Brazil). From the analysis of a set of bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells. This results in significantly improved initial virus⋅⋅⋅cell molecular recognition and attachment at the microscopic level, which trigger the infectious cycle.
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Affiliation(s)
- Santiago A. Gómez
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
| | - Natalia Rojas‐Valencia
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
- Escuela de Ciencias y HumanidadesDepartamento de Ciencias B'ásicasUniversidad Eafit AA3300MedellínColombia
| | - Sara Gómez
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Chiara Cappelli
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Albeiro Restrepo
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52–21050010MedellínColombia
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9
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Lafiosca P, Gómez S, Giovannini T, Cappelli C. Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach. J Chem Theory Comput 2022; 18:1765-1779. [PMID: 35184553 PMCID: PMC8908768 DOI: 10.1021/acs.jctc.1c01066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
We report on the
first formulation of a novel polarizable QM/MM
approach, where the density functional tight binding (DFTB) is coupled
to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ)
is then extended to the linear response within the TD-DFTB framework
and challenged to study absorption spectra of large condensed-phase
systems.
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Affiliation(s)
- Piero Lafiosca
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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10
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Todorov P, Georgieva S, Staneva D, Peneva P, Grozdanov P, Nikolova I, Grabchev I. Synthesis of New Modified with Rhodamine B Peptides for Antiviral Protection of Textile Materials. Molecules 2021; 26:molecules26216608. [PMID: 34771015 PMCID: PMC8587962 DOI: 10.3390/molecules26216608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/11/2023] Open
Abstract
Here we report on the synthesis and characterization of three new N-modified analogues of hemorphin-4 with rhodamine B. Modified with chloroacetyl, chloride cotton fabric has been dyed and color coordinates of the obtained textile materials were determined. Antiviral and virucidal activities of both the peptide-rhodamine B compounds and the dyed textile material were studied. Basic physicochemical properties (acid-base behavior, solvent influence, kinetics) related to the elucidation of structural activity of the new modified peptides based on their steric open/closed ring effect were studied. The obtained results lead to the conclusion that in protic solvent with change in pH of the environment, direct control over the dyeing of textiles can be achieved. Both the new hybrid peptide compounds and the modification of functionalized textile materials with these bioactive hemorphins showed virucidal activity against the human respiratory syncytial virus (HRSV-S2) and human adenovirus serotype 5 (HAdV-5) for different time intervals (30 and 60 min) and the most active compound was Rh-3.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
- Correspondence: ; Tel.: +359-2-8163423
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Desislava Staneva
- Department of Textile and Leathers, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Petia Peneva
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria;
| | - Petar Grozdanov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.G.); (I.N.)
| | - Ivanka Nikolova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (P.G.); (I.N.)
| | - Ivo Grabchev
- Faculty of Medicine, Sofia University “St. Kl. Ohridski”, 1407 Sofia, Bulgaria;
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Quemé-Peña M, Juhász T, Kohut G, Ricci M, Singh P, Szigyártó IC, Papp ZI, Fülöp L, Beke-Somfai T. Membrane Association Modes of Natural Anticancer Peptides: Mechanistic Details on Helicity, Orientation, and Surface Coverage. Int J Mol Sci 2021; 22:ijms22168613. [PMID: 34445319 PMCID: PMC8395313 DOI: 10.3390/ijms22168613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Anticancer peptides (ACPs) could potentially offer many advantages over other cancer therapies. ACPs often target cell membranes, where their surface mechanism is coupled to a conformational change into helical structures. However, details on their binding are still unclear, which would be crucial to reach progress in connecting structural aspects to ACP action and to therapeutic developments. Here we investigated natural helical ACPs, Lasioglossin LL-III, Macropin 1, Temporin-La, FK-16, and LL-37, on model liposomes, and also on extracellular vesicles (EVs), with an outer leaflet composition similar to cancer cells. The combined simulations and experiments identified three distinct binding modes to the membranes. Firstly, a highly helical structure, lying mainly on the membrane surface; secondly, a similar, yet only partially helical structure with disordered regions; and thirdly, a helical monomeric form with a non-inserted perpendicular orientation relative to the membrane surface. The latter allows large swings of the helix while the N-terminal is anchored to the headgroup region. These results indicate that subtle differences in sequence and charge can result in altered binding modes. The first two modes could be part of the well-known carpet model mechanism, whereas the newly identified third mode could be an intermediate state, existing prior to membrane insertion.
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Affiliation(s)
- Mayra Quemé-Peña
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
- Hevesy György Ph.D. School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Tünde Juhász
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
- Correspondence: (T.J.); (T.B.-S.)
| | - Gergely Kohut
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
- Hevesy György Ph.D. School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Maria Ricci
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
| | - Priyanka Singh
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
- Hevesy György Ph.D. School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Imola Cs. Szigyártó
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
| | - Zita I. Papp
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.I.P.); (L.F.)
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.I.P.); (L.F.)
| | - Tamás Beke-Somfai
- Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (M.Q.-P.); (G.K.); (M.R.); (P.S.); (I.C.S.)
- Correspondence: (T.J.); (T.B.-S.)
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12
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Menard LM, Wood NB, Vigoreaux JO. Secondary Structure of the Novel Myosin Binding Domain WYR and Implications within Myosin Structure. BIOLOGY 2021; 10:603. [PMID: 34209926 PMCID: PMC8301185 DOI: 10.3390/biology10070603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 01/05/2023]
Abstract
Structural changes in the myosin II light meromyosin (LMM) that influence thick filament mechanical properties and muscle function are modulated by LMM-binding proteins. Flightin is an LMM-binding protein indispensable for the function of Drosophila indirect flight muscle (IFM). Flightin has a three-domain structure that includes WYR, a novel 52 aa domain conserved throughout Pancrustacea. In this study, we (i) test the hypothesis that WYR binds the LMM, (ii) characterize the secondary structure of WYR, and (iii) examine the structural impact WYR has on the LMM. Circular dichroism at 260-190 nm reveals a structural profile for WYR and supports an interaction between WYR and LMM. A WYR-LMM interaction is supported by co-sedimentation with a stoichiometry of ~2.4:1. The WYR-LMM interaction results in an overall increased coiled-coil content, while curtailing ɑ helical content. WYR is found to be composed of 15% turns, 31% antiparallel β, and 48% 'other' content. We propose a structural model of WYR consisting of an antiparallel β hairpin between Q92-K114 centered on an ASX or β turn around N102, with a G1 bulge at G117. The Drosophila LMM segment used, V1346-I1941, encompassing conserved skip residues 2-4, is found to possess a traditional helical profile but is interpreted as having <30% helical content by multiple methods of deconvolution. This low helicity may be affiliated with the dynamic behavior of the structure in solution or the inclusion of a known non-helical region in the C-terminus. Our results support the hypothesis that WYR binds the LMM and that this interaction brings about structural changes in the coiled-coil. These studies implicate flightin, via the WYR domain, for distinct shifts in LMM secondary structure that could influence the structural properties and stabilization of the thick filament, scaling to modulation of whole muscle function.
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Affiliation(s)
| | | | - Jim O. Vigoreaux
- Department of Biology, University of Vermont, Burlington, VT 05405, USA; (L.M.M.); (N.B.W.)
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13
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Kohut G, Juhász T, Quemé-Peña M, Bősze SE, Beke-Somfai T. Controlling Peptide Function by Directed Assembly Formation: Mechanistic Insights Using Multiscale Modeling on an Antimicrobial Peptide-Drug-Membrane System. ACS OMEGA 2021; 6:15756-15769. [PMID: 34179620 PMCID: PMC8223213 DOI: 10.1021/acsomega.1c01114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/01/2021] [Indexed: 05/16/2023]
Abstract
Owing to their potential applicability against multidrug-resistant bacteria, antimicrobial peptides (AMPs) or host defense peptides (HDPs) gain increased attention. Besides diverse immunomodulatory roles, their classical mechanism of action mostly involves membrane disruption of microbes. Notably, their unbalanced overexpression has also been associated with host cell cytotoxicity in various diseases. Relatedly, AMPs can be subject to aggregate formation, either via self-assembly or together with other compounds, which has demonstrated a modulation effect on their biological functions, thus highly relevant both for drug targeting projects and understanding their in vivo actions. However, the molecular aspects of the related assembly formation are not understood. Here, we focused in detail on an experimentally studied AMP-drug system, i.e., CM15-suramin, and performed all-atom and coarse-grain (CG) simulations. Results obtained for all systems were in close line with experimental observations and indicate that the CM15-suramin aggregation is an energetically favorable and dynamic process. In the presence of bilayers, the peptide-drug assembly formation was highly dependent on lipid composition, and peptide aggregates themselves were also capable of binding to the membranes. Interestingly, longer CG simulations with zwitterionic membranes indicated an intermediate state in the presence of both AMP-drug assemblies and monomeric peptides located on the membrane surface. In sharp contrast, larger AMP-drug aggregates could not be detected with a negatively charged membrane, rather the AMPs penetrated its surface in a monomeric form, in line with previous in vitro observations. Considering experimental and theoretical results, it is promoted that in biological systems, cationic AMPs may often form associates with anionic compounds in a reversible manner, resulting in lower bioactivity. This is only mildly affected by zwitterionic membranes; however, membranes with a negative charge strongly alter the energetic preference of AMP assemblies, resulting in the dissolution of the complexes into the membrane. The phenomenon observed here at a molecular level can be followed in several experimental systems studied recently, where peptides interact with food colors, drug molecules, or endogenous compounds, which strongly indicates that reversible associate formation is a general phenomenon for these complexes. These results are hoped to be exploited in novel therapeutic strategies aiming to use peptides as drug targets and control AMP bioactivity by directed assembly formation.
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Affiliation(s)
- Gergely Kohut
- Institute
of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
- Hevesy
György PhD School of Chemistry, ELTE
Eötvös Loránd University, Pázmány Péter sétány
1/A, H-1117 Budapest, Hungary
| | - Tünde Juhász
- Institute
of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Mayra Quemé-Peña
- Institute
of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
- Hevesy
György PhD School of Chemistry, ELTE
Eötvös Loránd University, Pázmány Péter sétány
1/A, H-1117 Budapest, Hungary
| | - Szilvia Erika Bősze
- ELKH
Research Group of Peptide Chemistry, Eötvös
Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Tamás Beke-Somfai
- Institute
of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
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14
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Miranda AS, Marcos PM, Ascenso JR, Robalo MP, Bonifácio VDB, Berberan-Santos MN, Hickey N, Geremia S. Conventional vs. Microwave- or Mechanically-Assisted Synthesis of Dihomooxacalix[4]arene Phthalimides: NMR, X-ray and Photophysical Analysis. Molecules 2021; 26:molecules26061503. [PMID: 33801929 PMCID: PMC7998390 DOI: 10.3390/molecules26061503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
Direct O-alkylation of p-tert-butyldihomooxacalix[4]arene (1) with N-(bromopropyl)- or N-(bromoethyl)phthalimides and K2CO3 in acetonitrile was conducted under conventional heating (reflux) and using microwave irradiation and ball milling methodologies. The reactions afforded mono- and mainly distal di-substituted derivatives in the cone conformation, in a total of eight compounds. They were isolated by column chromatography, and their conformations and the substitution patterns were established by NMR spectroscopy (1H, 13C, COSY and NOESY experiments). The X-ray structures of four dihomooxacalix[4]arene phthalimide derivatives (2a, 3a, 3b and 5a) are reported, as well as their photophysical properties. The microwave (MW)-assisted alkylations drastically reduced the reaction times (from days to less than 45 min) and produced higher yields of both 1,3-di-substituted phthalimides (3a and 6a) with higher selectivity. Ball milling did not reveal to be a good method for this kind of reaction.
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Affiliation(s)
- Alexandre S. Miranda
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, 1749-016 Lisboa, Portugal;
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (V.D.B.B.); (M.N.B.-S.)
| | - Paula M. Marcos
- Centro de Química Estrutural, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, 1749-016 Lisboa, Portugal;
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Correspondence:
| | - José R. Ascenso
- Centro de Química Estrutural, Instituto Superior Técnico, Complexo I, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (J.R.A.); (M.P.R.)
| | - M. Paula Robalo
- Centro de Química Estrutural, Instituto Superior Técnico, Complexo I, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (J.R.A.); (M.P.R.)
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
| | - Vasco D. B. Bonifácio
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (V.D.B.B.); (M.N.B.-S.)
| | - Mário N. Berberan-Santos
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (V.D.B.B.); (M.N.B.-S.)
| | - Neal Hickey
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (N.H.); (S.G.)
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (N.H.); (S.G.)
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15
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Gómez SA, Rojas‐Valencia N, Gómez S, Egidi F, Cappelli C, Restrepo A. Binding of SARS-CoV-2 to Cell Receptors: A Tale of Molecular Evolution. Chembiochem 2020; 22:724-732. [PMID: 32986926 PMCID: PMC7537057 DOI: 10.1002/cbic.202000618] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/26/2020] [Indexed: 12/31/2022]
Abstract
The magnified infectious power of the SARS‐CoV‐2 virus compared to its precursor SARS‐CoV is intimately linked to an enhanced ability in the mutated virus to find available hydrogen‐bond sites in the host cells. This characteristic is acquired during virus evolution because of the selective pressure exerted at the molecular level. We pinpoint the specific residue (in the virus) to residue (in the cell) contacts during the initial recognition and binding and show that the virus⋅⋅⋅cell interaction is mainly due to an extensive network of hydrogen bonds and to a large surface of noncovalent interactions. In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus⋅⋅⋅cell interacting residues yields significant shifts of Δλmax=47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively.
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Affiliation(s)
- Santiago A. Gómez
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia
| | - Natalia Rojas‐Valencia
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia
- Escuela de Ciencias y HumanidadesDepartamento de Ciencias BásicasUniversidad EafitAA3300MedellínColombia
| | - Sara Gómez
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Franco Egidi
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Chiara Cappelli
- Scuola Normale SuperioreClasse di ScienzePiazza dei Cavalieri 756126PisaItaly
| | - Albeiro Restrepo
- Instituto de QuímicaUniversidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia
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16
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Passaretti P, Khan I, Dafforn TR, Goldberg Oppenheimer P. Improvements in the production of purified M13 bacteriophage bio-nanoparticle. Sci Rep 2020; 10:18538. [PMID: 33122639 PMCID: PMC7596064 DOI: 10.1038/s41598-020-75205-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/13/2020] [Indexed: 11/17/2022] Open
Abstract
M13 bacteriophage is a well-established versatile nano-building block, which can be employed to produce novel self-assembled functional materials and devices. Sufficient production and scalability of the M13, often require a large quantity of the virus and thus, improved propagation methods characterised by high capacity and degree of purity are essential. Currently, the 'gold-standard' is represented by infecting Escherichia coli cultures, followed by precipitation with polyethylene glycol (PEG). However, this is considerably flawed by the accumulation of contaminant PEG inside the freshly produced stocks, potentially hampering the reactivity of the individual M13 filaments. Our study demonstrates the effectiveness of implementing an isoelectric precipitation procedure to reduce the residual PEG along with FT-IR spectroscopy as a rapid, convenient and effective analytic validation method to detect the presence of this contaminant in freshly prepared M13 stocks.
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Affiliation(s)
- Paolo Passaretti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Inam Khan
- School of Metallurgy and Materials, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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17
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Rocha S, Kumar R, Horvath I, Wittung-Stafshede P. Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity. Protein Eng Des Sel 2020; 32:59-66. [PMID: 31566224 PMCID: PMC6908820 DOI: 10.1093/protein/gzz021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/19/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022] Open
Abstract
α-Synuclein misfolding results in the accumulation of amyloid fibrils in Parkinson’s disease. Missense protein mutations (e.g. A53T) have been linked to early onset disease. Although α-synuclein interacts with synaptic vesicles in the brain, it is not clear what role they play in the protein aggregation process. Here, we compare the effect of small unilamellar vesicles (lipid composition similar to synaptic vesicles) on wild-type (WT) and A53T α-synuclein aggregation. Using biophysical techniques, we reveal that binding affinity to the vesicles is similar for the two proteins, and both interact with the helix long axis parallel to the membrane surface. Still, the vesicles affect the aggregation of the variants differently: effects on secondary processes such as fragmentation dominate for WT, whereas for A53T, fibril elongation is mostly affected. We speculate that vesicle interactions with aggregate intermediate species, in addition to monomer binding, vary between WT and A53T, resulting in different consequences for amyloid formation.
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Affiliation(s)
- Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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18
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Potential anticonvulsant activity of novel VV-hemorphin-7 analogues containing unnatural amino acids: synthesis and characterization. Amino Acids 2020; 52:567-585. [PMID: 32206933 DOI: 10.1007/s00726-020-02836-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 10/24/2022]
Abstract
Herein, some new analogues of VV-hemorphin-7, modified at position 4 and 7 by the unnatural amino acids followed the structure Val-Val-Tyr-Xxx-Trp-Thr-Yyy-Arg-Phe-NH2, where Xxx is Ac5c (1-aminocyclopentanecarboxylic acid) or Ac6c (1-aminocyclohexane carboxylic acid) and Yyy is Dap (diaminopropanoic acid) or Dab (diaminobutanoic acid), were synthesized, characterized and investigated for anticonvulsant activity. The new synthetic peptide analogues were prepared by standard solid-phase peptide synthesis-Fmoc chemistry. A single intracerebroventricular (i.c.v.) injection at doses of 5, 10, and 20 µg/10 µl, respectively, was given before evaluation with timed intravenous pentylenetetrazole (ivPTZ) infusion test and 6-Hz psychomotor seizure test in mice. The acute neurological toxicity was determined using the rotarod test. To explain the structure-active properties of the modified peptides, some physicochemical characteristic was obtained. The FT-IR spectra and their second derivatives of the amide I, II, and III bands of the peptides show ß-sheet structure conformation. The calculation of isoelectric points, by potentiometric determination of dissociated constants, is in the range from 9.79 to 10.84. This study, for the first time, also reported on the reduction-oxidative potentials of the guanidine at Arg-moiety on such kind of peptides containing arginine and tyrosine residues in different medium and electrode surface. The VV-hemorphin-7 analogues 4 and 5 were the most active against the ivPTZ test, with the effect comparable to that of peptide 1 used as a positive control. Except compound 8, all other tested peptide analogues were ineffective to raise the threshold for the clonic seizures. The peptide analogue 5 showed 100% protection in the 6-Hz test, while the other seven VV-hemorphin-7 analogues have dose-dependent activity against psychomotor seizures comparable to 1. The novel peptides did not show neurotoxicity in the rotarod test.
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19
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Wang G, Platas-Iglesias C, Angelovski G. Europium(III) Macrocyclic Chelates Appended with Tyrosine-based Chromophores and Di-(2-picolyl)amine-based Receptors: Turn-On Luminescent Chemosensors Selective to Zinc(II) Ions. Chempluschem 2020; 85:806-814. [PMID: 31967740 DOI: 10.1002/cplu.201900731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Indexed: 11/06/2022]
Abstract
Zinc ions play an important role in many biological processes in the human body. To selectively detect Zn2+ , two EuDO3A-based complexes (DO3A=1,4,7,10-tetraazacyclododecane-1,4,7-tricarboxylic acid) appended with tyrosine as a chromophore and di-(2-picolyl)amine (DPA) as the Zn2+ recognition moiety were developed as suitable luminescent sensors. Their luminescence intensity is affected by the photoinduced electron transfer mechanism. Upon addition of Zn2+ , both probes display an up to sevenfold enhancement in Eu3+ emission. Competition experiments demonstrated their specificity toward Zn2+ over other metal ions, while also revealing the nonspecificity of the derivatives lacking the DPA-moiety, thus confirming the essential role of the DPA for the recognition of Zn2+ . The induced emission changes of Eu3+ allow for precise quantitative analysis of Zn2+ , establishing these lanthanide-based complexes as viable chemosensors for biological applications.
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Affiliation(s)
- Gaoji Wang
- MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076, Tübingen, Germany
| | - Carlos Platas-Iglesias
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química Facultade de Ciencias, Universidade da Coruña, A Coruña, Galicia, Spain
| | - Goran Angelovski
- MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076, Tübingen, Germany
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20
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Aijaz A, Trawinski D, McKirgan S, Parekkadan B. Non-invasive cell counting of adherent, suspended and encapsulated mammalian cells using optical density. Biotechniques 2019; 68:35-40. [PMID: 31870165 PMCID: PMC7031820 DOI: 10.2144/btn-2019-0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In situ measurement to determine mammalian cell number in a non-invasive, non-destructive and reagent-free manner is needed to enable continuous cell manufacturing. An analytical method is presented for non-invasive cell counting by conducting multiwavelength spectral analysis of mammalian cells achieving a minimal detectable cell count of 62,500 at 295 nm. Light absorbance was insensitive to culture volume, giving an absolute cell count rather than a concentration. The activation state of cells was also considered. The study was extended to quantification within polymeric microcapsules as an advanced substrate for mammalian cell growth in bioreactor formats and resulted in an offset directly correlating with the absorbance maxima of the polymer. These studies provide feasibility for optical density as a simple end point to indirectly quantify mammalian cell number for continuous monitoring of cell cultures.
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Affiliation(s)
- Ayesha Aijaz
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ 08854, USA
| | - Dylan Trawinski
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ 08854, USA
| | - Scott McKirgan
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ 08854, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ 08854, USA
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21
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Honegger P, Steinhauser O. The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns. Phys Chem Chem Phys 2019; 22:212-222. [PMID: 31799520 DOI: 10.1039/c9cp04752b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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22
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Khatun S, Singh A, Pawar N, Gupta AN. Aggregation of amylin: Spectroscopic investigation. Int J Biol Macromol 2019; 133:1242-1248. [PMID: 31028814 DOI: 10.1016/j.ijbiomac.2019.04.167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022]
Abstract
Apart from its relevance to pathology, protein misfolding disease like Type-II Diabetes Mellitus, caused by amyloids of amylin protein has attracted more attention due to structural changes occurring during the aggregation process. We report extensive spectroscopy data of amylin during fibril formation through Raman, FTIR, CD, UV-vis absorption and photoluminescence (PL) spectroscopy. UV-vis and PL spectrum showed the sigmoidal growth of fibril with a lag time of ~2 days, which is consistent with earlier reported work using dynamic light scattering (DLS). Raman spectra revealed the formation of parallel and anti-parallel β-sheet from 0% to 20% with ageing (1st day to 21st day) at pH 6.5 ± 0.1. The results are corroborated by CD and FTIR data. These show the change in β-sheet by 23% at pH 6.5 ± 0.1, 26% at pH = 1.0 ± 0.1 and 30% at pH = 12 ± 0.1. It is also shown that the formation and conversion of other secondary structures into β-sheet is very sensitive towards the pH and ageing. The study may be used for the development of therapeutic strategies that could inhibit or even reverse the process of aggregation.
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Affiliation(s)
- Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Anurag Singh
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Nisha Pawar
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India.
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23
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Del Galdo S, Chandramouli B, Mancini G, Barone V. Assessment of Multi-Scale Approaches for Computing UV–Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches. J Chem Theory Comput 2019; 15:3170-3184. [DOI: 10.1021/acs.jctc.9b00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara Del Galdo
- Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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24
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Rode JE, Górecki M, Witkowski S, Frelek J. Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking. Phys Chem Chem Phys 2018; 20:22525-22536. [PMID: 30140796 DOI: 10.1039/c8cp02491j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.
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Affiliation(s)
- Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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25
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Gobeaux F, Wien F. Reversible Assembly of a Drug Peptide into Amyloid Fibrils: A Dynamic Circular Dichroism Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7180-7191. [PMID: 29772895 DOI: 10.1021/acs.langmuir.8b00094] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The common view on the amyloid fibril formation is that it is a multistep process that involves many oligomeric intermediate species, which leads to a high degree of polymorphism. This view derives from numerous kinetic studies whose vast majority was carried out with amyloid β fragments or other pathological amyloidogenic sequences. Yet, it is not clear whether the mechanisms inferred from these studies are universal and also apply to functional amyloids, in particular to peptide hormones which form reversible amyloid structures. In the present work, we study the self-assembly properties of atosiban, a nonapeptide drug, whose sequence is very close to those of the oxytocin and vasopressin hormones. We show that this very soluble peptide consistently self-assembles into 7 nm wide amyloid fibrils above a critical aggregation concentration (2-10 w/w % depending on the buffer conditions). The peptide system is characterized in details, from the monomeric to the assembled form, with osmotic concentration measurements, transmission electron microscopy, small-angle X-ray scattering, infrared and fluorescence spectroscopy, and circular dichroism (CD). We have followed in situ the fibril assembly with fluorescence and synchrotron radiation CD and noticed that the peptide undergoes conformational changes during the process. However, several lines of evidence point toward the association of monomers and dimers into fibrils without passing through oligomeric intermediate species contrary to what is usually reported for pathogenic amyloids. The native β-hairpin conformation of the monomer could explain the straightforward assembly. The tyrosine stacking is also shown to play an important role.
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Affiliation(s)
- Frédéric Gobeaux
- LIONS-NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay , 91191 Gif-sur-Yvette Cedex , France
| | - Frank Wien
- SOLEIL Synchrotron , Saint Aubin 91190 , France
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26
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Del Galdo S, Mancini G, Daidone I, Zanetti Polzi L, Amadei A, Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. J Comput Chem 2018; 39:1747-1756. [DOI: 10.1002/jcc.25351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Laura Zanetti Polzi
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma Tor Vergata, Via Della Ricerca Scientifica; Roma 00100 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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27
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Lin CY, Shieh MJ. Near-Infrared Fluorescent Dye-Decorated Nanocages to Form Grenade-like Nanoparticles with Dual Control Release for Photothermal Theranostics and Chemotherapy. Bioconjug Chem 2018; 29:1384-1398. [PMID: 29505243 DOI: 10.1021/acs.bioconjchem.8b00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recently, nanoparticles (NPs) have been widely investigated for delivery of anticancer drugs. Here, a dual control drug-release modality was developed that uses naturally occurring protein apoferritin loaded with doxorubicin (DOX) and ADS-780 near-infrared (NIR) fluorescent dye-decorated NPs (ADNIR NPs). ADNIR NPs act as a grenade to detonate the targeted tumor site following laser irradiation (photothermal therapy, PTT) and explode into cluster warheads (apoferritin-loaded DOX nanocages, AF-DOX NCs) that further destroy the tumor cells (chemotherapy). Light was shown to disrupt the grenade-like structure of NPs to release AF-DOX NCs as well as DOX from NCs in low-pH intercellular environments. In vitro and in vivo studies showed that the structure of AF-DOX NCs was disassembled to release DOX, which then killed the cancer cells in organelles with acidic environments. In vivo studies showed that the ADNIR NP-decorated with NIR dye facilitated tracking of the accumulated NPs at the tumor site using an IVIS imaging system. Overall, targeted ADNIR NPs with dual-release mechanisms were developed for use in photothermal theranostic and chemotherapy. This modality has high potential for application in cancer treatment and clinical translation for drug delivery and imaging.
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Affiliation(s)
- Chun-Yen Lin
- Institute of Biomedical Engineering, College of Medicine and College of Engineering , National Taiwan University , No. 1, Section 1, Jen-Ai Road , Taipei 100 , Taiwan
| | - Ming-Jium Shieh
- Institute of Biomedical Engineering, College of Medicine and College of Engineering , National Taiwan University , No. 1, Section 1, Jen-Ai Road , Taipei 100 , Taiwan.,Department of Oncology , National Taiwan University Hospital and College of Medicine , #7, Chung-Shan South Road , Taipei 100 , Taiwan
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28
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Herburger A, van der Linde C, Beyer MK. Photodissociation spectroscopy of protonated leucine enkephalin. Phys Chem Chem Phys 2018; 19:10786-10795. [PMID: 28233882 DOI: 10.1039/c6cp08436b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated leucine enkephalin (YGGFL) was studied by ultraviolet photodissociation (UVPD) from 225 to 300 nm utilizing an optical parametric oscillator tunable wavelength laser system (OPO). Fragments were identified by absolute mass measurement in a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Bond cleavage was preferred in the vicinity of the two aromatic residues, resulting in high ion abundances for a4, a1, b3, y2 and y1 fragments. a, b and y ions dominated the mass spectrum, and full sequence coverage was achieved for those types. Photodissociation was most effective at the short wavelength end of the studied range, which is assigned to the onset of the La π-π* transition of the tyrosine chromophore, but worked well also at the Lb π-π* chromophore absorption maxima in the 35 000-39 000 cm-1 region. Several side-chain and internal fragments were observed. H atom loss is observed only above 41 000 cm-1, consistent with the requirement of a curve crossing to a repulsive 1πσ* state. It is suggested that the photochemically generated mobile H atom plays a role in further backbone cleavages, similar to the mechanism for electron capture dissociation. The b4 fragment is most intense at the Lb chromophore absorptions, undergoing additional fragmentation at higher photon energies. The high resolution of the FT-ICR MS revealed that out of all x and z-type fragments only x3 and x4 were formed, with low intensity. Other previously reported x- and z-fragments were re-assigned to internal fragments, based on exact mass measurement.
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Affiliation(s)
- Andreas Herburger
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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29
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Szigyártó IC, Deák R, Mihály J, Rocha S, Zsila F, Varga Z, Beke-Somfai T. Flow Alignment of Extracellular Vesicles: Structure and Orientation of Membrane-Associated Bio-macromolecules Studied with Polarized Light. Chembiochem 2018; 19:545-551. [PMID: 29237098 DOI: 10.1002/cbic.201700378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/17/2017] [Indexed: 12/26/2022]
Abstract
Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular-level properties, membrane-protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red-blood-cell-derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular-level structural information on these systems. Flow-linear dichroism (flow-LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane-protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.
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Affiliation(s)
- Imola Cs Szigyártó
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary
| | - Róbert Deák
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, Chemical Biology, Kemigården 4, 41296, Göteborg, Sweden
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary.,Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, 1094, Budapest, Hungary
| | - Tamás Beke-Somfai
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519, Budapest, Hungary.,Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Kemigården 4, 41296, Göteborg, Sweden
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30
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Honegger P, Steinhauser O. Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation. Phys Chem Chem Phys 2018; 20:22932-22945. [DOI: 10.1039/c8cp03422b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mechanism of depolarization in reverse micelles with zwitterionic surfactants and containing polar species but lacking ions is reported.
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Affiliation(s)
- Philipp Honegger
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
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31
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Honegger P, Schmollngruber M, Steinhauser O. Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions. Phys Chem Chem Phys 2018; 20:19581-19594. [DOI: 10.1039/c8cp02360c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive computational studies of ubiquitin crowding with a special focus on protein hydration directly visible in dielectric spectra.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Michael Schmollngruber
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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32
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Carrillo-Parramon O, Del Galdo S, Aschi M, Mancini G, Amadei A, Barone V. Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. J Chem Theory Comput 2017; 13:5506-5514. [DOI: 10.1021/acs.jctc.7b00341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá di L’Aquila, Via
Vetoio s.n.c.67100, L’Aquila, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, Universitá di Roma ’Tor Vergata’, Via Della Ricerca Scientifica, 00100 Roma, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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33
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Ruggenthaler M, Grass J, Schuh W, Huber C, Reischl R. Impurity profiling of liothyronine sodium by means of reversed phase HPLC, high resolution mass spectrometry, on-line H/D exchange and UV/Vis absorption. J Pharm Biomed Anal 2017; 143:147-158. [DOI: 10.1016/j.jpba.2017.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 03/28/2017] [Accepted: 05/23/2017] [Indexed: 11/28/2022]
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34
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Nag L, Sournia P, Myllykallio H, Liebl U, Vos MH. Identification of the TyrOH •+ Radical Cation in the Flavoenzyme TrmFO. J Am Chem Soc 2017; 139:11500-11505. [PMID: 28745052 DOI: 10.1021/jacs.7b04586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tyrosine (TyrOH) and tryptophan radicals play important roles as intermediates in biochemical charge-transfer reactions. Tryptophanyl radicals have been observed both in their protonated cation form and in their unprotonated neutral form, but to date, tyrosyl radicals have only been observed in their unprotonated form. With a genetically modified form of the flavoenzyme TrmFO as a suitable model system and using ultrafast fluorescence and absorption spectroscopy, we characterize its protonated precursor TyrOH•+, and we show this species to have a distinct visible absorption band and a transition moment that we suggest to lie close to the phenol symmetry axis. TyrOH•+ is formed in ∼1 ps by electron transfer to excited flavin and decays in ∼3 ps by charge recombination. These findings imply that TyrOH oxidation does not necessarily induce its concerted deprotonation. Our results will allow disentangling of photoproduct states in flavoproteins in often-encountered complex situations and more generally are important for understanding redox chains relying on tyrosyl intermediates.
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Affiliation(s)
- Lipsa Nag
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Pierre Sournia
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
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35
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Farkas V, Jákli I, Tóth GK, Perczel A. Aromatic Cluster Sensor of Protein Folding: Near-UV Electronic Circular Dichroism Bands Assigned to Fold Compactness. Chemistry 2016; 22:13871-13883. [PMID: 27504963 DOI: 10.1002/chem.201602455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 11/10/2022]
Abstract
Both far- and near-UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far-UV range), Lb bands (near-UV range) are applicable as 3D-fold sensors of protein's core structure. In this study we show that both Lb (Tyr) and Lb (Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross-validation, also provided here. The ensemble of 204 ECD spectra of Trp-cage miniproteins is analysed as a training set for "calibrating" Trp↔Tyr folded systems of known NMR structure. While in the far-UV ECD spectra changes are linear as a function of the temperature, near-UV ECD data indicate a non-linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding↔unfolding mechanism. We found that the Lb293 band is reporting on the 3D-structure compactness. In addition, the pure near-UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp↔Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase-inhibitor etc.) can now be analysed with higher confidence.
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Affiliation(s)
- Viktor Farkas
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány P. sétány 1A, 1117, Budapest, Hungary
| | - Imre Jákli
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány P. sétány 1A, 1117, Budapest, Hungary
| | - Gábor K Tóth
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, 6720, Szeged, Hungary
| | - András Perczel
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány P. sétány 1A, 1117, Budapest, Hungary. .,Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. sétány 1A, 1117, Budapest, Hungary.
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36
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Antosiewicz JM, Shugar D. UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 1: basic principles and properties of tyrosine chromophore. Biophys Rev 2016; 8:151-161. [PMID: 28510058 PMCID: PMC4884207 DOI: 10.1007/s12551-016-0198-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/17/2016] [Indexed: 11/08/2022] Open
Abstract
Spectroscopic properties of tyrosine residues may be employed in structural studies of proteins. Here we discuss several different types of UV–Vis spectroscopy, like normal, difference and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, and corresponding optical properties of the tyrosine chromophore, phenol, which are used to study protein structure.
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Affiliation(s)
- Jan M Antosiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - David Shugar
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
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37
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UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications. Biophys Rev 2016; 8:163-177. [PMID: 28510057 PMCID: PMC4884208 DOI: 10.1007/s12551-016-0197-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/07/2022] Open
Abstract
In Part 2 we discuss application of several different types of UV–Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.
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38
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Mu T, Chen S, Zhang Y, Guo P, Chen H. Determining the orientation of transition moments and depolarization by fluorescence polarizing angle spectrum. OPTICS EXPRESS 2015; 23:11748-11754. [PMID: 25969265 DOI: 10.1364/oe.23.011748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper, fluorescence polarizing angle spectrum, combined with degree of polarization(DOP), is proposed to determine the spatial orientation of transition dipole moments (TDMs) and depolarization of chlorophyll in solution. It is found that, due to the oriented TDMs under polarized laser excitation, the projections of angle of polarization(AOP) and DOP on the three orthogonal planes are different from each other. Experiments demonstrate that we can acquire the spatial orientation by detecting the projections of AOP on two orthogonal planes (xOz and yOz). Meanwhile, The depolarization can also be determined by the DOP spectrums. The validity of this method has been verified by another projection on the xOy plane.
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39
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Orientation of aromatic residues in amyloid cores: structural insights into prion fiber diversity. Proc Natl Acad Sci U S A 2014; 111:17158-63. [PMID: 25404291 DOI: 10.1073/pnas.1415663111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.
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