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Neira JL, Rizzuti B, Abian O, Velazquez-Campoy A. Isolated auto-citrullinated regions of PADI4 associate to the intact protein without altering their disordered conformation. Biophys Chem 2024; 312:107288. [PMID: 38991454 DOI: 10.1016/j.bpc.2024.107288] [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: 01/17/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024]
Abstract
PADI4 is one of the human isoforms of a group of enzymes intervening in the conversion of arginine to citrulline. It is involved in the development of several types of tumors, as well as other immunological illnesses, such as psoriasis, multiple sclerosis, or rheumatoid arthritis. PADI4 auto-citrullinates in several regions of its sequence, namely in correspondence of residues Arg205, Arg212, Arg218, and Arg383. We wanted to study whether the citrullinated moiety affects the conformation of nearby regions and its binding to intact PADI4. We designed two series of synthetic peptides comprising either the wild-type or the relative citrullinated versions of such regions - i.e., a first series of peptides comprising the first three arginines, and a second series comprising Arg383. We studied their conformational properties in isolation by using fluorescence, far-ultraviolet (UV) circular dichroism (CD), and 2D1H NMR. Furthermore, we characterized the binding of the wild-type and citrullinated peptides in the two series to the intact PADI4, by using isothermal titration calorimetry (ITC), fluorescence, and biolayer interferometry (BLI), as well as by molecular docking simulations. We observed that citrullination did not alter the local conformational propensities of the isolated peptides. Nevertheless, for all the peptides in the two series, citrullination slowed down the kinetic koff rates of the binding reaction to PADI4, probably due to differences in electrostatic effects compared to the presence of arginine. The affinities of PADI4 for unmodified peptides were slightly larger than those of the corresponding citrullinated ones in the two series, but they were all within the same range, indicating that there were no relevant variations in the thermodynamics of binding due to sequence effects. These results highlight details of the self-citrullination of PADI4 and, more generally, of possible auto-catalytic mechanisms taking place in vivo for other citrullinating enzymes or, alternatively, in proteins undergoing citrullination passively.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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2
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La Manna S, Cugudda A, Mercurio FA, Leone M, Fortuna S, Di Natale C, Lagreca E, Netti PA, Panzetta V, Marasco D. PEGylated SOCS3 Mimetics Encapsulated into PLGA-NPs as Selective Inhibitors of JAK/STAT Pathway in TNBC Cells. Int J Nanomedicine 2024; 19:7237-7251. [PMID: 39050870 PMCID: PMC11268778 DOI: 10.2147/ijn.s441205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction SOCS3 (suppressor of cytokine signaling 3) protein is a crucial regulator of cytokine-induced inflammation, and its administration has been shown to have therapeutic effects. Recently, we designed a chimeric proteomimetic of SOCS3, mimicking the interfacing regions of a ternary complex composed of SOCS3, JAK2 (Janus kinase 2) and gp130 (glycoprotein 130) proteins. The derived chimeric peptide, KIRCONG chim, demonstrated limited mimetic function owing to its poor water solubility. Methods We report investigations concerning a PEGylated variant of KIRCONG mimetic, named KIRCONG chim, bearing a PEG (Polyethylene glycol) moiety as a linker of noncontiguous SOCS3 regions. Its ability to bind to the catalytic domain of JAK2 was evaluated through MST (MicroScale Thermophoresis), as well as its stability in biological serum assays. The structural features of the cyclic compounds were investigated by CD (circular dichroism), nuclear magnetic resonance (NMR), and molecular dynamic (MD) studies. To evaluate the cellular effects, we employed a PLGA-nanoparticle as a delivery system after characterization using DLS and SEM techniques. Results KIRCONG chim PEG-revealed selective penetration into triple-negative breast cancer (TNBC) MDA-MB-231 cells with respect to the human breast epithelial cell line (MCF10A), acting as a potent inhibitor of STAT3 phosphorylation. Discussion Overall, the data indicated that miniaturization of the SOCS3 protein is a promising therapeutic approach for aberrant dysregulation of JAK/STAT during cancer progression.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
| | - Alessia Cugudda
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, 80131, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Genova, 16152, Italy
| | - Concetta Di Natale
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Elena Lagreca
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Paolo Antonio Netti
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Valeria Panzetta
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
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3
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Gampp O, Kadavath H, Riek R. NMR tools to detect protein allostery. Curr Opin Struct Biol 2024; 86:102792. [PMID: 38428364 DOI: 10.1016/j.sbi.2024.102792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Allostery is a fundamental mechanism of cellular homeostasis by intra-protein communication between distinct functional sites. It is an internal process of proteins to steer interactions not only with each other but also with other biomolecules such as ligands, lipids, and nucleic acids. In addition, allosteric regulation is particularly important in enzymatic activities. A major challenge in structural and molecular biology today is unraveling allosteric sites in proteins, to elucidate the detailed mechanism of allostery and the development of allosteric drugs. Here we summarize the recently developed tools and approaches which enable the elucidation of regulatory hotspots and correlated motion in biomolecules, focusing primarily on solution-state nuclear magnetic resonance spectroscopy (NMR). These tools open an avenue towards a rational understanding of the mechanism of allostery and provide essential information for the design of allosteric drugs.
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Affiliation(s)
- Olivia Gampp
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland; St. Jude Children's Research Hospital, 262 Danny Thomas Place, 38105 Memphis, Tennessee, USA. https://twitter.com/harijik
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland.
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4
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Neira JL, Palomino-Schätzlein M, Rejas V, Traverso JA, Rico M, López-Gorgé J, Chueca A, Cámara-Artigas A. Three-dimensional solution structure, dynamics and binding of thioredoxin m from Pisum sativum. Int J Biol Macromol 2024; 262:129781. [PMID: 38296131 DOI: 10.1016/j.ijbiomac.2024.129781] [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: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Thioredoxins (TRXs) are ubiquitous small, globular proteins involved in cell redox processes. In this work, we report the solution structure of TRX m from Pisum sativum (pea), which has been determined on the basis of 1444 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the 20 best structures for the backbone residues (Val7-Glu102) was 1.42 ± 0.15 Å, and 1.97 ± 0.15 Å when all heavy atoms were considered. The structure corresponds to the typical fold of TRXs, with a central five-stranded β-sheet flanked by four α-helices. Some residues had an important exchange dynamic contribution: those around the active site; at the C terminus of β-strand 3; and in the loop preceding α-helix 4. Smaller NOE values were observed at the N and C-terminal residues forming the elements of the secondary structure or, alternatively, in the residues belonging to the loops between those elements. A peptide derived from pea fructose-1,6-biphosphatase (FBPase), comprising the preceding region to the regulatory sequence of FBPase (residues Glu152 to Gln179), was bound to TRX m with an affinity in the low micromolar range, as measured by fluorescence and NMR titration experiments. Upon peptide addition, the intensities of the cross-peaks of all the residues of TRX m were affected, as shown by NMR. The value of the dissociation constant of the peptide from TRX m was larger than that of the intact FBPase, indicating that there are additional factors in other regions of the polypeptide chain of the latter protein affecting the binding to thioredoxin.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Martina Palomino-Schätzlein
- ProtoQSAR SL, CEEI-Valencia. Parque Tecnológico de Valencia, Av. Benjamin Franklin 12 (Dep. 8), 46980 Paterna, Valencia, Spain
| | - Virginia Rejas
- Centro de Investigación Príncipe Felipe, Calle de Eduardo Primo Yufera 3, 46012, Valencia, Spain
| | - José A Traverso
- Department of Cell Biology, Faculty of Science, University of Granada, 18001 Granada, Spain
| | - Manual Rico
- Instituto de Quimica Física Blas Cabrera (CSIC), Calle Serrano 119, 28006 Madrid, Spain
| | - Julio López-Gorgé
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Prof. Albareda 1, 18008 Granada, Spain
| | - Ana Chueca
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), Prof. Albareda 1, 18008 Granada, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain
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5
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Bartholow T, Burroughs PW, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells. ACS CENTRAL SCIENCE 2024; 10:199-208. [PMID: 38292613 PMCID: PMC10823516 DOI: 10.1021/acscentsci.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
The cell surface proteome (surfaceome) plays a pivotal role in virtually all extracellular biology, and yet we are only beginning to understand the protein complexes formed in this crowded environment. Recently, a high-resolution approach (μMap) was described that utilizes multiple iridium-photocatalysts attached to a secondary antibody, directed to a primary antibody of a protein of interest, to identify proximal neighbors by light-activated conversion of a biotin-diazirine to a highly reactive carbene followed by LC/MS (Geri, J. B.; Oakley, J. V.; Reyes-Robles, T.; Wang, T.; McCarver, S. J.; White, C. H.; Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C. Science2020, 367, 1091-1097). Here we calibrated the spatial resolution for carbene labeling using site-specific conjugation of a single photocatalyst to a primary antibody drug, trastuzumab (Traz), in complex with its structurally well-characterized oncogene target, HER2. We observed relatively uniform carbene labeling across all amino acids, and a maximum distance of ∼110 Å from the fixed photocatalyst. When targeting HER2 overexpression cells, we identified 20 highly enriched HER2 neighbors, compared to a nonspecific membrane tethered catalyst. These studies identify new HER2 interactors and calibrate the radius of carbene photoprobe labeling for the surfaceome.
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Affiliation(s)
- Thomas
G. Bartholow
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Paul W.W. Burroughs
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Susanna K. Elledge
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Lisa L. Kirkemo
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Virginia Garda
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Kevin K. Leung
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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6
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Huang PJJ, Evans NM, Lu C, Li AZ, Dieckmann T, Liu J. Cross-Binding of Adenosine by Aptamers Selected Using Theophylline. Chembiochem 2023; 24:e202300566. [PMID: 37747943 DOI: 10.1002/cbic.202300566] [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: 08/11/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 09/27/2023]
Abstract
We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20-fold lower affinities. This discovery led to the current work to examine the cross-binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross-binding to adenosine was observed, and the affinity was 18 to 38-fold lower for adenosine based on assays using isothermal titration calorimetry and ThT fluorescence spectroscopy. The binding complexes were characterized using NMR spectroscopy, and both adenosine and theophylline showed an overall similar binding structure to the DNA theophylline aptamer, although small differences were also observed. In contrast, the RNA aptamer did not show binding to adenosine, although both aptamers have very similar relative selectivity for various methylxanthines including caffeine. After a negative selection, a few new aptamers with completely different primary sequences for theophylline were obtained and they did not show binding to adenosine. Thus, there are many ways for aptamers to bind theophylline and some can have cross-binding to adenosine. In biology, theophylline, caffeine, and adenosine can bind to the same protein receptors to regulate sleep, and their binding to the same DNA motifs may suggest an early role of nucleic acids in similar regulatory functions.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Natasha M Evans
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Chang Lu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
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7
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Tam JP, Huang J, Loo S, Li Y, Kam A. Ginsentide-like Coffeetides Isolated from Coffee Waste Are Cell-Penetrating and Metal-Binding Microproteins. Molecules 2023; 28:6556. [PMID: 37764332 PMCID: PMC10538209 DOI: 10.3390/molecules28186556] [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: 08/10/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Coffee processing generates a huge amount of waste that contains many natural products. Here, we report the discovery of a panel of novel cell-penetrating and metal ion-binding microproteins designated coffeetide cC1a-c and cL1-6 from the husk of two popular coffee plants, Coffea canephora and Coffea liberica, respectively. Combining sequence determination and a database search, we show that the prototypic coffeetide cC1a is a 37-residue, eight-cysteine microprotein with a hevein-like cysteine motif, but without a chitin-binding domain. NMR determination of cC1a reveals a compact structure that confers its resistance to heat and proteolytic degradation. Disulfide mapping together with chemical synthesis reveals that cC1a has a ginsentide-like, and not a hevein-like, disulfide connectivity. In addition, transcriptomic analysis showed that the 98-residue micrcoproten-like coffeetide precursor contains a three-domain arrangement, like ginsentide precursors. Molecular modeling, together with experimental validation, revealed a Mg2+ and Fe3+ binding pocket at the N-terminus formed by three glutamic acids. Importantly, cC1a is amphipathic with a continuous stretch of 19 apolar amino acids, which enables its cell penetration to target intracellular proteins, despite being highly negatively charged. Our findings suggest that coffee by-products could provide a source of ginsentide-like bioactive peptides that have the potential to target intracellular proteins.
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Affiliation(s)
- James P. Tam
- Synthetic Enzymes and Natural Products Center, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (J.H.); (S.L.); (Y.L.); (A.K.)
| | - Jiayi Huang
- Synthetic Enzymes and Natural Products Center, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (J.H.); (S.L.); (Y.L.); (A.K.)
| | - Shining Loo
- Synthetic Enzymes and Natural Products Center, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (J.H.); (S.L.); (Y.L.); (A.K.)
- Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yimeng Li
- Synthetic Enzymes and Natural Products Center, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (J.H.); (S.L.); (Y.L.); (A.K.)
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Antony Kam
- Synthetic Enzymes and Natural Products Center, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (J.H.); (S.L.); (Y.L.); (A.K.)
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China
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8
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Mosseri A, Sancho-Albero M, Mercurio FA, Leone M, De Cola L, Romanelli A. Tryptophan-PNA gc Conjugates Self-Assemble to Form Fibers. Bioconjug Chem 2023; 34:1429-1438. [PMID: 37486977 PMCID: PMC10436247 DOI: 10.1021/acs.bioconjchem.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Indexed: 07/26/2023]
Abstract
Peptide nucleic acids and their conjugates to peptides can self-assemble and generate complex architectures. In this work, we explored the self-assembly of PNA dimers conjugated to the dipeptide WW. Our studies suggest that the indole ring of tryptophan promotes aggregation of the conjugates. The onset of fluorescence is observed upon self-assembly. The structure of self-assembled WWgc is concentration-dependent, being spherical at low concentrations and fibrous at high concentrations. As suggested by molecular modeling studies, fibers are stabilized by stacking interactions between tryptophans and Watson-Crick hydrogen bonds between nucleobases.
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Affiliation(s)
- Andrea Mosseri
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
| | - María Sancho-Albero
- Department
of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy
| | - Flavia Anna Mercurio
- Istituto
di Biostrutture e Bioimmagini—CNR, via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Istituto
di Biostrutture e Bioimmagini—CNR, via Pietro Castellino 111, 80131 Naples, Italy
| | - Luisa De Cola
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy
| | - Alessandra Romanelli
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
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9
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Bartholow TG, Burroughs P, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Site-specific proximity labeling at single residue resolution for identification of protein partners in vitro and on cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550738. [PMID: 37546992 PMCID: PMC10402114 DOI: 10.1101/2023.07.27.550738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cell surface proteome, or surfaceome, is encoded by more than 4000 genes, but we are only beginning to understand the complexes they form. Rapid proximity labeling around specific membrane targets allows for capturing weak and transient interactions expected in the crowded and dynamic environment of the surfaceome. Recently, a high-resolution approach called μMap has been described (Geri, J. B., Oakley, J. V., Reyes-Robles, T., Wang, T., McCarver, S. J., White, C. H., Rodriguez-Rivera, F. P., Parker, D. L., Hett, E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020) Science 367 , 1091-1097) in which an iridium (Ir)-based photocatalyst is attached to a specific antibody to target labeling of neighbors utilizing light-activated generation of carbenes from diazirine compounds via Dexter Energy Transfer (DET). Here we studied and optimized the spatial resolution for the method using an oncoprotein complex between the antibody drug, trastuzumab (Traz), and its target HER2. A set of eight single site-specific Ir-catalytic centers were engineered into Traz to study intra- and inter-molecular labeling in vitro and on cells by mass spectrometry. From this structurally well-characterized complex we observed a maximum distance of ∼110 Å for labeling. Labeling occurred almost uniformly over the full range of amino acids, unlike the residue specific labeling of other techniques. To examine on cell labeling that is specific to HER2 as opposed to simply being on the membrane, we compared the labeling patterns for the eight Traz-catalyst species to random labeling of membrane proteins using a metabolically integrated fatty acid catalyst. Our results identified 20 high confidence HER2 neighbors, many novel, that were more than 6-fold enriched compared to the non-specific membrane tethered catalyst. These studies define distance labeling parameters from single-site catalysts placed directly on the membrane target of interest, and more accurately compare to non-specific labeling to identify membrane complexes with higher confidence.
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10
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Mambelli F, Marinho FV, Andrade JM, de Araujo ACVSC, Abuna RPF, Fabri VMR, Santos BPO, da Silva JS, de Magalhães MTQ, Homan EJ, Leite LCC, Dias GB, Heck N, Mendes DAGB, Mansur DS, Báfica A, Oliveira SC. Recombinant Bacillus Calmette-Guérin Expressing SARS-CoV-2 Chimeric Protein Protects K18-hACE2 Mice against Viral Challenge. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1925-1937. [PMID: 37098890 PMCID: PMC10247535 DOI: 10.4049/jimmunol.2200731] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
COVID-19 has accounted for more than 6 million deaths worldwide. Bacillus Calmette-Guérin (BCG), the existing tuberculosis vaccine, is known to induce heterologous effects over other infections due to trained immunity and has been proposed to be a potential strategy against SARS-CoV-2 infection. In this report, we constructed a recombinant BCG (rBCG) expressing domains of the SARS-CoV-2 nucleocapsid and spike proteins (termed rBCG-ChD6), recognized as major candidates for vaccine development. We investigated whether rBCG-ChD6 immunization followed by a boost with the recombinant nucleocapsid and spike chimera (rChimera), together with alum, provided protection against SARS-CoV-2 infection in K18-hACE2 mice. A single dose of rBCG-ChD6 boosted with rChimera associated with alum elicited the highest anti-Chimera total IgG and IgG2c Ab titers with neutralizing activity against SARS-CoV-2 Wuhan strain when compared with control groups. Importantly, following SARS-CoV-2 challenge, this vaccination regimen induced IFN-γ and IL-6 production in spleen cells and reduced viral load in the lungs. In addition, no viable virus was detected in mice immunized with rBCG-ChD6 boosted with rChimera, which was associated with decreased lung pathology when compared with BCG WT-rChimera/alum or rChimera/alum control groups. Overall, our study demonstrates the potential of a prime-boost immunization system based on an rBCG expressing a chimeric protein derived from SARS-CoV-2 to protect mice against viral challenge.
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Affiliation(s)
- Fábio Mambelli
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fábio V. Marinho
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juvana M. Andrade
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana C. V. S. C. de Araujo
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo P. F. Abuna
- Platform of Bi-Institutional Research in Translational Medicine, Oswaldo Cruz Foundation-Fiocruz, Ribeirão Preto, São Paulo, Brazil
| | - Victor M. R. Fabri
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno P. O. Santos
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João S. da Silva
- Platform of Bi-Institutional Research in Translational Medicine, Oswaldo Cruz Foundation-Fiocruz, Ribeirão Preto, São Paulo, Brazil
| | - Mariana T. Q. de Magalhães
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - E. Jane Homan
- ioGenetics LLC, Madison, Wisconsin, United States of America
| | | | - Greicy B.M. Dias
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Nicoli Heck
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Daniel A. G. B. Mendes
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Daniel S. Mansur
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - André Báfica
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Sergio C. Oliveira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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11
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Barbour A, Smith L, Oveisi M, Williams M, Huang RC, Marks C, Fine N, Sun C, Younesi F, Zargaran S, Orugunty R, Horvath TD, Haidacher SJ, Haag AM, Sabharwal A, Hinz B, Glogauer M. Discovery of phosphorylated lantibiotics with proimmune activity that regulate the oral microbiome. Proc Natl Acad Sci U S A 2023; 120:e2219392120. [PMID: 37216534 PMCID: PMC10235938 DOI: 10.1073/pnas.2219392120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/15/2023] [Indexed: 05/24/2023] Open
Abstract
Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) that are produced by bacteria. Interest in this group of natural products is increasing rapidly as alternatives to conventional antibiotics. Some human microbiome-derived commensals produce lantibiotics to impair pathogens' colonization and promote healthy microbiomes. Streptococcus salivarius is one of the first commensal microbes to colonize the human oral cavity and gastrointestinal tract, and its biosynthesis of RiPPs, called salivaricins, has been shown to inhibit the growth of oral pathogens. Herein, we report on a phosphorylated class of three related RiPPs, collectively referred to as salivaricin 10, that exhibit proimmune activity and targeted antimicrobial properties against known oral pathogens and multispecies biofilms. Strikingly, the immunomodulatory activities observed include upregulation of neutrophil-mediated phagocytosis, promotion of antiinflammatory M2 macrophage polarization, and stimulation of neutrophil chemotaxis-these activities have been attributed to the phosphorylation site identified on the N-terminal region of the peptides. Salivaricin 10 peptides were determined to be produced by S. salivarius strains found in healthy human subjects, and their dual bactericidal/antibiofilm and immunoregulatory activity may provide new means to effectively target infectious pathogens while maintaining important oral microbiota.
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Affiliation(s)
- Abdelahhad Barbour
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Leif Smith
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Morvarid Oveisi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - McKinley Williams
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Ruo Chen Huang
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Cara Marks
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Noah Fine
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Chunxiang Sun
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Fereshteh Younesi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Sina Zargaran
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | | | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Amarpreet Sabharwal
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Boris Hinz
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Department of Dental Oncology, Maxillofacial and Ocular Prosthetics, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
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12
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Manu VS, Olivieri C, Veglia G. Water irradiation devoid pulses enhance the sensitivity of 1H, 1H nuclear Overhauser effects. JOURNAL OF BIOMOLECULAR NMR 2023; 77:1-14. [PMID: 36534224 DOI: 10.1007/s10858-022-00407-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 05/03/2023]
Abstract
The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the structures of medium-to-large size biomolecules and characterize protein-protein, protein-RNA, protein-DNA, and protein-ligand interactions in aqueous solutions. Typical [1H,1H] NOESY pulse sequences incorporate water suppression schemes to reduce the water signal that dominates 1H-detected spectra and minimize NOE intensity losses due to unwanted polarization exchange between water and labile protons. However, at high- and ultra-high magnetic fields, the excitation of the water signal during the execution of the NOESY pulse sequences may cause significant attenuation of NOE cross-peak intensities. Using an evolutionary algorithm coupled with artificial intelligence, we recently designed high-fidelity pulses [Water irrAdiation DEvoid (WADE) pulses] that elude water excitation and irradiate broader bandwidths relative to commonly used pulses. Here, we demonstrate that WADE pulses, implemented into the 2D [1H,1H] NOESY experiments, increase the intensity of the NOE cross-peaks for labile and, to a lesser extent, non-exchangeable protons. We applied the new 2D [1H,1H] WADE-NOESY pulse sequence to two well-folded, medium-size proteins, i.e., the K48C mutant of ubiquitin and the Raf kinase inhibitor protein. We observed a net increase of the NOE intensities varying from 30 to 170% compared to the commonly used NOESY experiments. The new WADE pulses can be easily engineered into 2D and 3D homo- and hetero-nuclear NOESY pulse sequences to boost their sensitivity.
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Affiliation(s)
- V S Manu
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 139 Smith Hall, Pleasant St. SE, Minneapolis, MN, 55455, USA.
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13
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Vink S, Akondi KB, Jin J, Poth K, Torres AM, Kuchel PW, Burke SL, Head GA, Alewood PF. Taipan Natriuretic Peptides Are Potent and Selective Agonists for the Natriuretic Peptide Receptor A. Molecules 2023; 28:molecules28073063. [PMID: 37049825 PMCID: PMC10095932 DOI: 10.3390/molecules28073063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/14/2023] Open
Abstract
Cardiovascular ailments are a major cause of mortality where over 1.3 billion people suffer from hypertension leading to heart-disease related deaths. Snake venoms possess a broad repertoire of natriuretic peptides with therapeutic potential for treating hypertension, congestive heart failure, and related cardiovascular disease. We now describe several taipan (Oxyuranus microlepidotus) natriuretic peptides TNPa-e which stimulated cGMP production through the natriuretic peptide receptor A (NPR-A) with higher potencies for the rat NPR-A (rNPR-A) over human NPR-A (hNPR-A). TNPc and TNPd were the most potent, demonstrating 100- and 560-fold selectivity for rNPR-A over hNPR-A. In vivo studies found that TNPc decreased diastolic and systolic blood pressure (BP) and increased heart rate (HR) in conscious normotensive rabbits, to a level that was similar to that of human atrial natriuretic peptide (hANP). TNPc also enhanced the bradycardia due to cardiac afferent stimulation (Bezold-Jarisch reflex). This indicated that TNPc possesses the ability to lower blood pressure and facilitate cardiac vagal afferent reflexes but unlike hANP does not produce tachycardia. The 3-dimensional structure of TNPc was well defined within the pharmacophoric disulfide ring, displaying two turn-like regions (RMSD = 1.15 Å). Further, its much greater biological stability together with its selectivity and potency will enhance its usefulness as a biological tool.
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Affiliation(s)
- Simone Vink
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Kalyana Bharati Akondi
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Jean Jin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Kim Poth
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Allan M Torres
- Nanoscale Organisation and Dynamics Group, Western Sydney University, Penrith 2759, Australia
| | - Philip W Kuchel
- School of Life and Environmental Sciences, University of Sydney, Sydney 2006, Australia
| | - Sandra L Burke
- Baker Heart and Diabetes Institute, Melbourne 3004, Australia
| | - Geoffrey A Head
- Baker Heart and Diabetes Institute, Melbourne 3004, Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
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14
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Neira JL, Palomino-Schätzlein M. Folding of the nascent polypeptide chain of a histidine phosphocarrier protein in vitro. Arch Biochem Biophys 2023; 736:109538. [PMID: 36738980 DOI: 10.1016/j.abb.2023.109538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The phosphotransferase system (PTS), a metabolic pathway formed by five proteins, modulates the use of sugars in bacteria. The second protein in the chain is the histidine phosphocarrier, HPr, with the binding site at His15. The HPr kinase/phosphorylase (HPrK/P), involved in the bacterial use of carbon sources, phosphorylates HPr at Ser46, and it binds at its binding site. The regulator of sigma D protein (Rsd) also binds to HPr at His15. We have designed fragments of HPr, growing from its N-terminus and containing the His15. In this work, we obtained three fragments, HPr38, HPr58 and HPr70, comprising the first thirty-eight, fifty-eight and seventy residues of HPr, respectively. All fragments were mainly disordered, with evidence of a weak native-like, helical population around the binding site, as shown by fluorescence, far-ultraviolet circular dichroism, size exclusion chromatography and nuclear magnetic resonance. Although HPr38, HPr58 and HPr70 were disordered, they could bind to: (i) the N-terminal domain of first protein of the PTS, EIN; (ii) Rsd; and, (iii) HPrK/P, as shown by fluorescence and biolayer interferometry (BLI). The association constants for each protein to any of the fragments were in the low micromolar range, within the same range than those measured in the binding of HPr to each protein. Then, although acquisition of stable, native-like secondary and tertiary structures occurred at the last residues of the polypeptide, the ability to bind protein partners happened much earlier in the growing chain. Binding was related to the presence of the native-like structure around His15.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - Martina Palomino-Schätzlein
- ProtoQSAR SL, CEEI-Valencia, Parque Tecnológico de Valencia, Av. Benjamin Franklin 12 (Dep. 8), 46980, Paterna, Valencia, Spain
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15
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Dissanayake GC, Ndi CN, Markley JL, Martinez JB, Hanson PR. Total Synthesis of Sanctolide A and Formal Synthesis of (2 S)-Sanctolide A. J Org Chem 2023; 88:805-817. [PMID: 36602547 DOI: 10.1021/acs.joc.2c01922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two synthetic strategies employing phosphate tether-mediated one-pot sequential protocols for the total synthesis of the polyketide nonribosomal peptide macrolide, sanctolide A, and the formal synthesis of the (2S)-epimer of sanctolide A are reported. In this work, a phosphate tether-mediated one-pot sequential ring-closing metathesis/cross metathesis/substrate-controlled "H2"/tether removal approach was developed to accomplish the total synthesis of the natural product sanctolide A.
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Affiliation(s)
- Gihan C Dissanayake
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045-7582, United States
| | - Cornelius N Ndi
- Department of Chemistry, University of Kansas, 1140 Gray-Little Hall, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Jana L Markley
- Department of Chemistry, University of Kansas, 1140 Gray-Little Hall, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - James B Martinez
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045-7582, United States
| | - Paul R Hanson
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045-7582, United States
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16
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McKay RT. Metabolomics and NMR. Handb Exp Pharmacol 2023; 277:73-116. [PMID: 36355220 DOI: 10.1007/164_2022_616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The purpose of this manuscript will be to convince the reader to dive deeper into NMR spectroscopy and prevent the technique from being just another "black-box" in the lab. We will try to concisely highlight interesting topics and supply additional references for further exploration at each stage. The advantages of delving into the technique will be shown. The secondary objective, i.e., avoiding common problems before starting, will hopefully then become clear. Lastly, we will emphasize the spectrometer information needed for manuscript reporting to allow reproduction of results and confirm findings.
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Affiliation(s)
- Ryan T McKay
- Department Chemistry, College of Natural and Applied Sciences, University of Alberta, Edmonton, AB, Canada.
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17
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Geng M, Hansanant N, Lu SE, Lockless SW, Shin R, Orugunty R, Smith L. Synthesis and characterization of semisynthetic analogs of the antifungal occidiofungin. Front Microbiol 2022; 13:1056453. [PMID: 36583054 PMCID: PMC9792986 DOI: 10.3389/fmicb.2022.1056453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Occidiofungin is a broad-spectrum antifungal compound produced by Burkholderia contaminans MS14. It is a cyclic glycol-lipopeptide with a novel beta-amino acid (NAA2) containing a hydroxylated C18 fatty acid chain with a xylose sugar. This study reports a strategy to produce semisynthetic analogs of occidiofungin to further explore the structure activity relationships of this class of compounds. Oxidative cleavage of the diol present on carbons five C(5) and six C(6) removes the xylose and twelve carbons of the fatty acid chain. The resulting cyclic peptide product, occidiofungin aldehyde, is devoid of antifungal activity. However, the free aldehyde group on this product can be subjected to reductive amination reactions to provide interesting semisynthetic analogs. This chemistry allows the quick generation of analogs to study the structure activity relationships of this class of compounds. Despite restoring the length of the aliphatic side chain by reductive amination addition with undecylamine or dodecylamine to the free aldehyde group, the obtained analogs did not demonstrate any antifungal activity. The antifungal activity was partially restored by the addition of a DL-dihydrosphingosine. The dodecylamine analog was demonstrated to still bind to the cellular target actin, suggesting that the diol on the side chain of native occidiofungin is important for entry into the cell enabling access to cellular target F-actin. These results show that the alkyl side chain on NAA2 along with the diol present on this side chain is important for occidiofungin's antifungal activity.
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Affiliation(s)
- Mengxin Geng
- Department of Biology, Texas A&M University, College Station, TX, United States,Sano Chemicals Inc., Bryan, TX, United States
| | - Nopakorn Hansanant
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States
| | - Steve W. Lockless
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Ronald Shin
- Central Alabama High-Field NMR Facility, Structural Biology Shared Facility, Cancer Center University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Leif Smith
- Department of Biology, Texas A&M University, College Station, TX, United States,Sano Chemicals Inc., Bryan, TX, United States,*Correspondence: Leif Smith,
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18
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Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248762. [PMID: 36557898 PMCID: PMC9786777 DOI: 10.3390/molecules27248762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis.
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19
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Rizzuti B, Iovanna JL, Neira JL. Deciphering the Binding of the Nuclear Localization Sequence of Myc Protein to the Nuclear Carrier Importin α3. Int J Mol Sci 2022; 23:ijms232315333. [PMID: 36499669 PMCID: PMC9739371 DOI: 10.3390/ijms232315333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The oncoprotein Myc is a transcription factor regulating global gene expression and modulating cell proliferation, apoptosis, and metabolism. Myc has a nuclear localization sequence (NLS) comprising residues Pro320 to Asp328, to allow for nuclear translocation. We designed a peptide comprising such region and the flanking residues (Ala310-Asn339), NLS-Myc, to study, in vitro and in silico, the ability to bind importin α3 (Impα3) and its truncated species (ΔImpα3) depleted of the importin binding domain (IBB), by using fluorescence, circular dichroism (CD), biolayer interferometry (BLI), nuclear magnetic resonance (NMR), and molecular simulations. NLS-Myc interacted with both importin species, with affinity constants of ~0.5 µM (for Impα3) and ~60 nM (for ΔImpα3), as measured by BLI. The molecular simulations predicted that the anchoring of NLS-Myc took place in the major binding site of Impα3 for the NLS of cargo proteins. Besides clarifying the conformational behavior of the isolated NLS of Myc in solution, our results identified some unique properties in the binding of this localization sequence to the nuclear carrier Impα3, such as a difference in the kinetics of its release mechanism depending on the presence or absence of the IBB domain.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: (B.R.); (J.L.N.)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
- Correspondence: (B.R.); (J.L.N.)
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20
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Agadi N, Maity A, Jha AK, Chakrabarti R, Kumar A. Distinct mode of membrane interaction and disintegration by diverse class of antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184047. [PMID: 36100074 DOI: 10.1016/j.bbamem.2022.184047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 12/29/2022]
Abstract
The exploitation of conventional antibiotics in conjunction with the adeptness of microbes has led to the emergence of multi-drug-resistant pathogens. This has posed a severe threat to combating life-threatening infectious diseases. Antimicrobial peptides (AMP), which are considered to be the first line of defense in all living organisms, are being developed for therapeutic use. Herein, we determined the NMR solution structure of Rhesus macaque Myeloid Alpha Defensin-4 (RMAD4), a defensin AMP. Additionally, the distinct modes of membrane perturbation for two structurally dissimilar classes of AMPs was studied using biophysical methods namely, Solid-state 31P NMR, DSC and cryo-TEM. The cathelicidin - Bovine myeloid antimicrobial peptide (BMAP-28 (1-18)), which adopts a helical conformation, and the defensin RMAD4 peptide that natively folds to form β-sheets appeared to engage differently with the bacterial membrane. The helical BMAP-28 (1-18) peptide initiates lipid segregation and membrane thinning followed by pore formation, while the β-stranded RMAD4 peptide demonstrates fragmentation of the bilayer by the carpet or detergent-like mechanism of action. Molecular dynamics studies sufficiently corroborated these findings. The structure and mechanism of action of the AMPs studied using experimental and computational approaches are believed to help in providing a platform for the rational design of new competent and cost-effective antimicrobial peptides for therapeutic applications.
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Affiliation(s)
- Nutan Agadi
- Centre for Research in Nanotechnology and Science (CRNTS), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akash Kumar Jha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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21
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Insights into Network of Hot Spots of Aggregation in Nucleophosmin 1. Int J Mol Sci 2022; 23:ijms232314704. [PMID: 36499032 PMCID: PMC9736328 DOI: 10.3390/ijms232314704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
In a protein, point mutations associated with diseases can alter the native structure and provide loss or alteration of functional levels, and an internal structural network defines the connectivity among domains, as well as aggregate/soluble states' equilibria. Nucleophosmin (NPM)1 is an abundant nucleolar protein, which becomes mutated in acute myeloid leukemia (AML) patients. NPM1-dependent leukemogenesis, which leads to its aggregation in the cytoplasm (NPMc+), is still obscure, but the investigations have outlined a direct link between AML mutations and amyloid aggregation. Protein aggregation can be due to the cooperation among several hot spots located within the aggregation-prone regions (APR), often predictable with bioinformatic tools. In the present study, we investigated potential APRs in the entire NPM1 not yet investigated. On the basis of bioinformatic predictions and experimental structures, we designed several protein fragments and analyzed them through typical aggrsegation experiments, such as Thioflavin T (ThT), fluorescence and scanning electron microscopy (SEM) experiments, carried out at different times; in addition, their biocompatibility in SHSY5 cells was also evaluated. The presented data clearly demonstrate the existence of hot spots of aggregation located in different regions, mostly in the N-terminal domain (NTD) of the entire NPM1 protein, and provide a more comprehensive view of the molecular details potentially at the basis of NPMc+-dependent AML.
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22
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Fadeev M, O’Hagan MP, Biniuri Y, Willner I. Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes. J Phys Chem B 2022; 126:8931-8939. [PMID: 36315022 PMCID: PMC9661473 DOI: 10.1021/acs.jpcb.2c05624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.
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23
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Moreira Brito JC, Carvalho LR, Neves de Souza A, Carneiro G, Magalhães PP, Farias LM, Guimarães NR, Verly RM, Resende JM, Elena de Lima M. PEGylation of the antimicrobial peptide LyeTx I-b maintains structure-related biological properties and improves selectivity. Front Mol Biosci 2022; 9:1001508. [PMID: 36310605 PMCID: PMC9611540 DOI: 10.3389/fmolb.2022.1001508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 07/31/2023] Open
Abstract
The biological activity of antimicrobial peptides and proteins is closely related to their structural aspects and is sensitive to certain post-translational modifications such as glycosylation, lipidation and PEGylation. However, PEGylation of protein and peptide drugs has expanded in recent years due to the reduction of their toxicity. Due to their size, the PEGylation process can either preserve or compromise the overall structure of these biopolymers and their biological properties. The antimicrobial peptide LyeTx I-bcys was synthesized by Fmoc strategy and coupled to polyethylene glycol 2.0 kDa. The conjugates were purified by HPLC and characterized by MALDI-ToF-MS analysis. Microbiological assays with LyeTx I-bcys and LyeTx I-bPEG were performed against Staphylococcus aureus (ATCC 33591) and Escherichia coli (ATCC 25922) in liquid medium. MIC values of 2.0 and 1.0 µM for LyeTx I-bcys and 8.0 and 4.0 µM for LyeTx I-bPEG were observed against S. aureus and E. coli, respectively. PEGylation of LyeTx I-bcys (LyeTx I-bPEG) decreased the cytotoxicity determined by MTT method for VERO cells compared to the non-PEGylated peptide. In addition, structural and biophysical studies were performed to evaluate the effects of PEGylation on the nature of peptide-membrane interactions. Surface Plasmon Resonance experiments showed that LyeTx I-b binds to anionic membranes with an association constant twice higher than the PEGylated form. The three-dimensional NMR structures of LyeTx I-bcys and LyeTx I-bPEG were determined and compared with the LyeTx I-b structure, and the hydrodynamic diameter and zeta potential of POPC:POPG vesicles were similar upon the addition of both peptides. The mPEG-MAL conjugation of LyeTx I-bcys gave epimers, and it, together with LyeTx I-bPEG, showed clear α-helical profiles. While LyeTx I-bcys showed no significant change in amphipathicity compared to LyeTx I-b, LyeTx I-bPEG was found to have a slightly less clear separation between hydrophilic and hydrophobic faces. However, the similar conformational freedom of LyeTx I-b and LyeTx I-bPEG suggests that PEGylation does not cause significant structural changes. Overall, our structural and biophysical studies indicate that the PEGylation does not alter the mode of peptide interaction and maintains antimicrobial activity while minimizing tissue toxicity, which confirmed previous results obtained in vivo. Interestingly, significantly improved proteolytic resistance to trypsin and proteinase K was observed after PEGylation.
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Affiliation(s)
| | - Lucas Raposo Carvalho
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Amanda Neves de Souza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Guilherme Carneiro
- Departamento de Farmácia, Faculdade de Ciências Biológicas e da Saúde, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Paula Prazeres Magalhães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luiz Macêdo Farias
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Natália Rocha Guimarães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo Moreira Verly
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Jarbas Magalhães Resende
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Elena de Lima
- Programa de Pós-graduação em Medicina e Biomedicina da Santa Casa de Belo Horizonte, Belo Horizonte, MG, Brazil
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Dembele H, Mating M, Singh R, Fatehi S, Herrera AI, Park Y, Prakash O. Ecdysis triggering hormone peptide in the African malaria mosquito Anopheles gambiae: The peptide structure for receptor activation. INSECT SCIENCE 2022; 29:1309-1317. [PMID: 35020973 PMCID: PMC9273798 DOI: 10.1111/1744-7917.13004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/14/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Infections by mosquito-borne diseases represent one of the leading causes of death in third world countries. The rapid progression of resistance to conventional insecticide causes a significant threat to the highly efficient preventive methods currently in place. Insect neuropeptidergic system offers potential targets to control the insect vectors. The essential roles of the neuropeptide ecdysis triggering hormone (ETH) in insect development and reproduction led us to attempt understanding of the fundamentals of the biochemical interaction between ETH and its receptor in the African malaria mosquito Anopheles gambiae. One of two ETH peptides of the African malaria mosquito (AgETH1), a small peptide hormone with 17 amino acid residues (SESPGFFIKLSKSVPRI-NH2 ), was studied to elucidate its molecular structure. N-termini deletions and mutations of conserved amino acids in the ligand revealed the critical residues for the receptor activation. The solution structure of AgETH1 using 2D 1 H-1 H nuclear magnetic resonance (NMR) spectroscopy and nuclear overhauser effect (NOE) derived constraints revealed a short alpha helix between residues 3S and 11S. The NMR solution structure of AgETH1 will be of significant assistance for designing a new class of insecticidal compounds that acts on the AgETH receptor aiming for in silico docking studies.
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Affiliation(s)
- Hawa Dembele
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansas66506
| | - Moritz Mating
- Department of EntomologyKansas State UniversityManhattanKansas66506
| | - Rupinder Singh
- Department of EntomologyKansas State UniversityManhattanKansas66506
| | - Soheila Fatehi
- Department of EntomologyKansas State UniversityManhattanKansas66506
| | - Alvaro I. Herrera
- Department of Chemistry & BiochemistryAuburn UniversityAuburnAlabamaUSA
| | - Yoonseong Park
- Department of EntomologyKansas State UniversityManhattanKansas66506
| | - Om Prakash
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansas66506
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25
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High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations. Int J Mol Sci 2022; 23:ijms231911039. [PMID: 36232339 PMCID: PMC9569650 DOI: 10.3390/ijms231911039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The crucial role of integrin in pathological processes such as tumor progression and metastasis formation has inspired intense efforts to design novel pharmaceutical agents modulating integrin functions in order to provide new tools for potential therapies. In the past decade, we have investigated the biological proprieties of the chimeric peptide RGDechi, containing a cyclic RGD motif linked to an echistatin C-terminal fragment, able to specifically recognize αvβ3 without cross reacting with αvβ5 and αIIbβ3 integrin. Additionally, we have demonstrated using two RGDechi-derived peptides, called RGDechi1-14 and ψRGDechi, that chemical modifications introduced in the C-terminal part of the peptide alter or abolish the binding to the αvβ3 integrin. Here, to shed light on the structural and dynamical determinants involved in the integrin recognition mechanism, we investigate the effects of the chemical modifications by exploring the conformational space sampled by RGDechi1-14 and ψRGDechi using an integrated natural-abundance NMR/MD approach. Our data demonstrate that the flexibility of the RGD-containing cycle is driven by the echistatin C-terminal region of the RGDechi peptide through a coupling mechanism between the N- and C-terminal regions.
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26
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La Manna S, Fortuna S, Leone M, Mercurio FA, Di Donato I, Bellavita R, Grieco P, Merlino F, Marasco D. Ad-hoc modifications of cyclic mimetics of SOCS1 protein: Structural and functional insights. Eur J Med Chem 2022; 243:114781. [PMID: 36152385 DOI: 10.1016/j.ejmech.2022.114781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
Suppressors of cytokine signaling 1 (SOCS1) protein, a negative regulator of the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway, possesses a small kinase inhibitory region (KIR) involved in the inhibition of JAK kinases. Several studies showed that mimetics of KIR-SOCS1 can be potent therapeutics in several disorders (e.g., neurological, autoimmune or cardiovascular diseases). In this work, starting from a recently identified cyclic peptidomimetic of KIR-SOCS1, icPS5(Nal1), to optimize the peptide structure and improve its biological activity, we designed novel derivatives, containing crucial amino acids substitutions and/or modifications affecting the ring size. By combining microscale thermophoresis (MST), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR) and computational studies, we showed that the cycle size plays a key role in the interaction with JAK2 and the substitution of native residues with un-natural building blocks is a valid tool to maintain low-micromolar affinity toward JAK2, greatly increasing their serum stability. These findings contribute to increase the structural knowledge required for the recognition of SOCS1/JAK2 and to progress towards their conversion into more drug-like compounds.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Sara Fortuna
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152, Genova, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, CNR, 80145, Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, CNR, 80145, Naples, Italy
| | - Ilaria Di Donato
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosa Bellavita
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
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27
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Human Enzyme PADI4 Binds to the Nuclear Carrier Importin α3. Cells 2022; 11:cells11142166. [PMID: 35883608 PMCID: PMC9319256 DOI: 10.3390/cells11142166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/13/2022] [Accepted: 07/08/2022] [Indexed: 12/18/2022] Open
Abstract
PADI4 is a peptidyl-arginine deiminase (PADI) involved in the conversion of arginine to citrulline. PADI4 is present in macrophages, monocytes, granulocytes, and several cancer cells. It is the only PADI family member observed within both the nucleus and the cytoplasm. PADI4 has a predicted nuclear localization sequence (NLS) comprising residues Pro56 to Ser83, to allow for nuclear translocation. Recent predictors also suggest that the region Arg495 to Ile526 is a possible NLS. To understand how PADI4 is involved in cancer, we studied the ability of intact PADI4 to bind importin α3 (Impα3), a nuclear transport factor that plays tumor-promoting roles in several cancers, and its truncated species (ΔImpα3) without the importin-binding domain (IBB), by using fluorescence, circular dichroism (CD), and isothermal titration calorimetry (ITC). Furthermore, the binding of two peptides, encompassing the first and the second NLS regions, was also studied using the same methods and molecular docking simulations. PADI4 interacted with both importin species, with affinity constants of ~1–5 µM. The isolated peptides also interacted with both importins. The molecular simulations predict that the anchoring of both peptides takes place in the major binding site of Impα3 for the NLS of cargo proteins. These findings suggest that both NLS regions were essentially responsible for the binding of PADI4 to the two importin species. Our data are discussed within the framework of a cell mechanism of nuclear transport that is crucial in cancer.
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28
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Mosseri A, Sancho‐Albero M, Leone M, Nava D, Secundo F, Maggioni D, De Cola L, Romanelli A. Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer. Chemistry 2022; 28:e202200693. [PMID: 35474351 PMCID: PMC9325372 DOI: 10.1002/chem.202200693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 11/17/2022]
Abstract
Self‐assembly of biomolecules such as peptides, nucleic acids or their analogues affords supramolecular objects, exhibiting structures and physical properties dependent on the amino‐acid or nucleobase composition. Conjugation of the peptide diphenylalanine (FF) to peptide nucleic acids triggers formation of self‐assembled structures, mainly stabilized by interactions between FF. In this work we report formation of homogeneous chiral fibers upon self‐assembly of the hybrid composed of the tetraphenylalanine peptide (4F) conjugated to the PNA dimer adenine‐thymine (at). In this case nucleobases seem to play a key role in determining the morphology and chirality of the fibers. When the PNA “at” is replaced by guanine‐cytosine dimer “gc”, disordered structures are observed. Spectroscopic characterization of the self‐assembled hybrids, along with AFM and SEM studies is reported. Finally, a structural model consistent with the experimental evidence has also been obtained, showing how the building blocks of 4Fat arrange to give helical fibers.
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Affiliation(s)
- Andrea Mosseri
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
| | - Maria Sancho‐Albero
- Department of Molecular Biochemistry and Pharmacology Istituto di Ricerche Farmacologiche Mario Negri IRCCS 20156 Milano Italy
| | - Marilisa Leone
- Istituto di Biostrutture e Bioimmagini – CNR via Mezzocannone 16 80134 Naples Italy
| | - Donatella Nava
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR via Mario Bianco 9 Milan 20131 Italy
| | - Daniela Maggioni
- Dipartimento di Chimica Università degli Studi di Milano Via Golgi 19 20133 Milano Italy
| | - Luisa De Cola
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
- Department of Molecular Biochemistry and Pharmacology Istituto di Ricerche Farmacologiche Mario Negri IRCCS 20156 Milano Italy
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
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29
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Petersingham G, Zaman MS, Johnson AJ, Reddy N, Torres AM, Wu MJ. Molecular details of aluminium-amyloid β peptide interaction by nuclear magnetic resonance. Biometals 2022; 35:759-769. [PMID: 35639270 DOI: 10.1007/s10534-022-00399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative condition that poses major challenges to human health. Both amyloid β (Aβ) and metal ions such as aluminium are implicated in the development of AD. By the means of NMR, the interactions of Al3+ with Aβ1-28 peptide as well as the Aβ1-28 analogues were studied, and the key binding sites of Al3+ in Aβ determined. NMR data showed Al3+ interacts with Aβ1-28 at the NH and αH of numerous residues by exhibiting upfield shifts. Using Aβ analogues where His6, His13 and His14 were individually replaced by alanine residue(s), including Aβ H6A, Aβ H13A, Aβ H14A, and Aβ H6,13,14A, the results demonstrated that the histidine residues (His6, His13 and His14) and N-terminal Asp1 were involved in the Al3+ coordination. These findings provide, for the first time, the details of the molecular interaction between Al3+ and Aβ, which points to the potential role of Al3+ in Aβ aggregation, hence in AD development.
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Affiliation(s)
- Gayani Petersingham
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Mohammad S Zaman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Adam J Johnson
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Narsimha Reddy
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Allan M Torres
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.,Nanoscale Organisation and Dynamics Group, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Ming J Wu
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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30
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Güntert P. A B-factor for NOEs? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107189. [PMID: 35358856 DOI: 10.1016/j.jmr.2022.107189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Nuclear Overhauser effects (NOEs) are influenced by motion. Here, we derive exact, analytical results for a model of isotropic, harmonic fluctuations of atom positions that corresponds to the one underlying crystallographic B-factors. The model includes steric repulsion and yields closed-form expressions for the expected value of general invertible functions of the distance between two atoms, with the special case r-6 for NOEs. We discuss the implications for the definition of an NOE-based B-factor in solution NMR.
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Affiliation(s)
- Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
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31
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Vincenzi M, Anna Mercurio F, Di Natale C, Palumbo R, Pirone L, La Manna S, Marasco D, Maria Pedone E, Leone M. Targeting Ship2-Sam with peptide ligands: Novel insights from a multidisciplinary approach. Bioorg Chem 2022; 122:105680. [DOI: 10.1016/j.bioorg.2022.105680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
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32
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La Manna S, Leone M, Mercurio FA, Florio D, Marasco D. Structure-Activity Relationship Investigations of Novel Constrained Chimeric Peptidomimetics of SOCS3 Protein Targeting JAK2. Pharmaceuticals (Basel) 2022; 15:ph15040458. [PMID: 35455455 PMCID: PMC9031227 DOI: 10.3390/ph15040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 03/31/2022] [Accepted: 04/07/2022] [Indexed: 12/03/2022] Open
Abstract
SOCS3 (suppressor of cytokine signaling 3) protein suppresses cytokine-induced inflammation and its deletion in neurons or immune cells increases the pathological growth of blood vessels. Recently, we designed several SOCS3 peptidomimetics by assuming as template structures the interfacing regions of the ternary complex constituted by SOCS3, JAK2 (Janus Kinase 2) and gp130 (glycoprotein 130) proteins. A chimeric peptide named KIRCONG chim, including non-contiguous regions demonstrated able to bind to JAK2 and anti-inflammatory and antioxidant properties in VSMCs (vascular smooth muscle cells). With the aim to improve drug-like features of KIRCONG, herein we reported novel cyclic analogues bearing different linkages. In detail, in two of them hydrocarbon cycles of different lengths were inserted at positions i/i+5 and i/i+7 to improve helical conformations of mimetics. Structural features of cyclic compounds were investigated by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopies while their ability to bind to catalytic domain of JAK2 was assessed through MST (MicroScale Thermophoresis) assay as well as their stability in biological serum. Overall data indicate a crucial role exerted by the length and the position of the cycle within the chimeric structure and could pave the way to the miniaturization of SOCS3 protein for therapeutic aims.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, Research Center on Bioactive Peptides (CIRPEB), University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.)
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), 80145 Naples, Italy; (M.L.); (F.A.M.)
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (CNR), 80145 Naples, Italy; (M.L.); (F.A.M.)
| | - Daniele Florio
- Department of Pharmacy, Research Center on Bioactive Peptides (CIRPEB), University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.)
| | - Daniela Marasco
- Department of Pharmacy, Research Center on Bioactive Peptides (CIRPEB), University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.)
- Correspondence: ; Tel.: +39-0812534607
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Structure Elucidation of Triterpenoid Saponins Found in an Immunoadjuvant Preparation of Quillaja brasiliensis Using Mass Spectrometry and 1H and 13C NMR Spectroscopy. Molecules 2022; 27:molecules27082402. [PMID: 35458600 PMCID: PMC9024837 DOI: 10.3390/molecules27082402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/02/2022] Open
Abstract
An immunoadjuvant preparation (named Fraction B) was obtained from the aqueous extract of Quillaja brasiliensis leaves, and further fractionated by consecutive separations with silica flash MPLC and reverse phase HPLC. Two compounds were isolated, and their structures elucidated using a combination of NMR spectroscopy and mass spectrometry. One of these compounds is a previously undescribed triterpene saponin (Qb1), which is an isomer of QS-21, the unique adjuvant saponin employed in human vaccines. The other compound is a triterpene saponin previously isolated from Quillaja saponaria bark, known as S13. The structure of Qb1 consists of a quillaic acid residue substituted with a β-d-Galp-(1→2)-[β-d-Xylp-(1→3)]-β-d-GlcpA trisaccharide at C3, and a β-d-Xylp-(1→4)-α-l-Rhap-(1→2)-[α-l-Arap-(1→3)]-β-d-Fucp moiety at C28. The oligosaccharide at C28 was further substituted at O4 of the fucosyl residue with an acyl group capped with a β-d-Xylp residue.
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Straat ME, Martinez-Tellez B, Nahon KJ, Janssen LG, Verhoeven A, van der Zee L, Mulder MT, Kooijman S, Boon MR, van Lennep JER, Cobbaert CM, Giera M, Rensen PC. nComprehensive (apo)lipoprotein profiling in patients with genetic hypertriglyceridemia using LC-MS and NMR spectroscopy. J Clin Lipidol 2022; 16:472-482. [DOI: 10.1016/j.jacl.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/05/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022]
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Yin G, Lv G, Zhang J, Jiang H, Lai T, Yang Y, Ren Y, Wang J, Yi C, Chen H, Huang Y, Xiao C. Early-stage structure-based drug discovery for small GTPases by NMR spectroscopy. Pharmacol Ther 2022; 236:108110. [PMID: 35007659 DOI: 10.1016/j.pharmthera.2022.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Small GTPase or Ras superfamily, including Ras, Rho, Rab, Ran and Arf, are fundamental in regulating a wide range of cellular processes such as growth, differentiation, migration and apoptosis. They share structural and functional similarities for binding guanine nucleotides and hydrolyzing GTP. Dysregulations of Ras proteins are involved in the pathophysiology of multiple human diseases, however there is still a stringent need for effective treatments targeting these proteins. For decades, small GTPases were recognized as 'undruggable' targets due to their complex regulatory mechanisms and lack of deep pockets for ligand binding. NMR has been critical in deciphering the structural and dynamic properties of the switch regions that are underpinning molecular switch functions of small GTPases, which pave the way for developing new effective inhibitors. The recent progress of drug or lead molecule development made for small GTPases profoundly delineated how modern NMR techniques reshape the field of drug discovery. In this review, we will summarize the progress of structural and dynamic studies of small GTPases, the NMR techniques developed for structure-based drug screening and their applications in early-stage drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guohua Lv
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Jerry Zhang
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Tianqi Lai
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Yushan Yang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Yong Ren
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Chenju Yi
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China; Research Institute of Xi'an Jiaotong University, Zhejiang, Hangzhou, Zhejiang Province 311215, PR China
| | - Yun Huang
- Howard Hughes Medical Institute, Chevy Chase 20815, MD, USA; Department of Physiology & Biophysics, Weill Cornell Medicine, New York 10065, NY, USA.
| | - Chaoni Xiao
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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Clay MC, Saleh T, Kamatham S, Rossi P, Kalodimos CG. Progress toward automated methyl assignments for methyl-TROSY applications. Structure 2022; 30:69-79.e2. [PMID: 34914892 PMCID: PMC8741727 DOI: 10.1016/j.str.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023]
Abstract
Methyl-TROSY spectroscopy has extended the reach of solution-state NMR to supra-molecular machineries over 100 kDa in size. Methyl groups are ideal probes for studying structure, dynamics, and protein-protein interactions in quasi-physiological conditions with atomic resolution. Successful implementation of the methodology requires accurate methyl chemical shift assignment, and the task still poses a significant challenge in the field. In this work, we outline the current state of technology for methyl labeling, data collection, data analysis, and nuclear Overhauser effect (NOE)-based automated methyl assignment approaches. We present MAGIC-Act and MAGIC-View, two Python extensions developed as part of the popular NMRFAM-Sparky package, and MAGIC-Net a standalone structure-based network analysis program. MAGIC-Act conducts statistically driven amino acid typing, Leu/Val pairing guided by 3D HMBC-HMQC, and NOESY cross-peak symmetry checking. MAGIC-Net provides model-based NOE statistics to aid in selection of a methyl labeling scheme. The programs provide a versatile, semi-automated framework for rapid methyl assignment.
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Affiliation(s)
- Mary C. Clay
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tamjeed Saleh
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Samuel Kamatham
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Paolo Rossi
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Corresponding authors: ,
| | - Charalampos G. Kalodimos
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Lead Contact,Corresponding authors: ,
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Biswas K, Bhunia A. Probing the Functional Interaction Interface of Lipopolysaccharide and Antimicrobial Peptides: A Solution-State NMR Perspective. Methods Mol Biol 2022; 2548:211-231. [PMID: 36151500 DOI: 10.1007/978-1-0716-2581-1_13] [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] [Indexed: 06/16/2023]
Abstract
Antimicrobial peptides (AMPs) have been a topic of substantial research as the next-generation antibiotics. They have been extensively studied for the selectivity and action against microbial membrane lipids in imparting their targeted functioning. To determine the effectivity of the peptides against the Gram-negative pathogens, it is imperative to elucidate their role in interacting with the lipopolysaccharide moieties. Lipopolysaccharide is a major component of the outer membrane of the Gram-negative bacteria. It serves to protect the bacteria as well as govern the functionality of several antibacterial agents. It can prevent the access of the agents into the inner membrane of the bacteria, thus rendering them inactive. Several techniques have been employed to study the interaction for better designing of peptides; NMR spectroscopy is one of the most widely used techniques in determining the interactive properties of peptides with LPS as it can provide the details in atomistic level. NMR spectroscopy provides information about the structural and conformational changes as well as the dynamics of the interactions.
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Affiliation(s)
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India.
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César Moreira Brito J, Gustavo Lima W, Magalhães Resende J, Cristina Sampaio de Assis D, Boff D, Nascimento Cardoso V, Almeida Amaral F, Maria Souza-Fagundes E, Odília Antunes Fernandes S, Elena de Lima M. Pegylated LyeTx I-b peptide is effective against carbapenem-resistant Acinetobacter baumannii in an in vivo model of pneumonia and shows reduced toxicity. Int J Pharm 2021; 609:121156. [PMID: 34624440 DOI: 10.1016/j.ijpharm.2021.121156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/27/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
The World Health Organization (WHO) has been warning about the importance of developing new drugs against superbugs. Antimicrobial peptides are an alternative in this context, most of them being involved in innate immunity, acting in various ways, and some even showing synergism with commercial antimicrobial agents. LyeTx I-b is a synthetic peptide derived from native LyeTx I, originally isolated from Lycosa erythrognatha spider venom. Although LyeTx I-b is active against several multidrug-resistant bacteria, it shows some hemolytic and cytotoxic effects. To overcome this hindrance, in the present study we PEGylated LyeTx I-b and evaluated its toxicity and in vitro and in vivo activities on pneumonia caused by multi-resistant Acinetobacter baumannii. PEGylated LyeTx I-b (LyeTx I-bPEG) maintained the same MIC value as the non- PEGylated peptide, showed anti-biofilm activity, synergistic effect with commercial antimicrobial agents, and did not induce resistance. Moreover, in vivo experiments showed its activity against pneumonia. Additionally, LyeTx I-bPEG reduced hemolysis up to 10 times, was approximately 2 times less cytotoxic to HEK-293 cells and 4 times less toxic to mice in acute toxicity models, compared to LyeTx I-b. Our results show LyeTx I-bPEG as a promising antimicrobial candidate, significantly active against pneumonia caused by multidrug-resistant A. baumannii.
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Affiliation(s)
- Júlio César Moreira Brito
- Programa de Inovação Tecnológica e Biofarmacêutica, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil; Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
| | - William Gustavo Lima
- Laboratório de Radioisótopos, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Campus Pampulha, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jarbas Magalhães Resende
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora Cristina Sampaio de Assis
- Escola de Veterinária, Departamento de Inspeção Sanitária, Campus Pampulha, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Daiane Boff
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Valbert Nascimento Cardoso
- Laboratório de Radioisótopos, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Campus Pampulha, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flávio Almeida Amaral
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine Maria Souza-Fagundes
- Programa de Inovação Tecnológica e Biofarmacêutica, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Simone Odília Antunes Fernandes
- Laboratório de Radioisótopos, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Campus Pampulha, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria Elena de Lima
- Programa de Inovação Tecnológica e Biofarmacêutica, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil; Faculdade Santa Casa de Belo Horizonte: Programa de Pós-Graduação em Medicina-Biomedicina, Belo Horizonte, Minas Gerais, Brazil.
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Novotný A, Novotný J, Kejnovská I, Vorlíčková M, Fiala R, Marek R. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Res 2021; 49:11425-11437. [PMID: 34718718 PMCID: PMC8599794 DOI: 10.1093/nar/gkab915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 11/12/2022] Open
Abstract
Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence-structure-stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
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Affiliation(s)
- Aleš Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Jan Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Radovan Fiala
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Radek Marek
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
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Timmons PB, Hewage CM. Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca. Sci Rep 2021; 11:22468. [PMID: 34789753 PMCID: PMC8599514 DOI: 10.1038/s41598-021-01769-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 01/13/2023] Open
Abstract
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.
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Affiliation(s)
- Patrick B Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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Ecsédi P, Gógl G, Nyitray L. Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes. Front Mol Biosci 2021; 8:749052. [PMID: 34708078 PMCID: PMC8542695 DOI: 10.3389/fmolb.2021.749052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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Diaferia C, Avitabile C, Leone M, Gallo E, Saviano M, Accardo A, Romanelli A. Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates. Chemistry 2021; 27:14307-14316. [PMID: 34314536 PMCID: PMC8597081 DOI: 10.1002/chem.202102481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/12/2022]
Abstract
Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the "suprastructures" typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.
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Affiliation(s)
- Carlo Diaferia
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR)Via Mezzocannone 1680134NaplesItaly
| | | | - Michele Saviano
- Institute of Crystallography (CNR)Via Amendola 12270126BariItaly
| | - Antonella Accardo
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | - Alessandra Romanelli
- Department of Pharmaceutical SciencesUniversity of MilanVia Venezian 2120133MilanItaly
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Residual Helicity at the Active Site of the Histidine Phosphocarrier, HPr, Modulates Binding Affinity to Its Natural Partners. Int J Mol Sci 2021; 22:ijms221910805. [PMID: 34639146 PMCID: PMC8509676 DOI: 10.3390/ijms221910805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022] Open
Abstract
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) modulates the preferential use of sugars in bacteria. The first proteins in the cascade are common to all organisms (EI and HPr). The active site of HPr involves a histidine (His15) located immediately before the beginning of the first α-helix. The regulator of sigma D (Rsd) protein also binds to HPr. The region of HPr comprising residues Gly9-Ala30 (HPr9–30), involving the first α-helix (Ala16-Thr27) and the preceding active site loop, binds to both the N-terminal region of EI and intact Rsd. HPr9–30 is mainly disordered. We attempted to improve the affinity of HPr9–30 to both proteins by mutating its sequence to increase its helicity. We designed peptides that led to a marginally larger population in solution of the helical structure of HPr9–30. Molecular simulations also suggested a modest increment in the helical population of mutants, when compared to the wild-type. The mutants, however, were bound with a less favorable affinity than the wild-type to both the N-terminal of EI (EIN) or Rsd, as tested by isothermal titration calorimetry and fluorescence. Furthermore, mutants showed lower antibacterial properties against Staphylococcus aureus than the wild-type peptide. Therefore, we concluded that in HPr, a compromise between binding to its partners and residual structure at the active site must exist to carry out its function.
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Wüthrich K. Brownian motion, spin diffusion and protein structure determination in solution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 331:107031. [PMID: 34391647 DOI: 10.1016/j.jmr.2021.107031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
This paper presents my recollections on the development of protein structure determination by NMR in solution from 1968 to 1992. The key to success was to identify NMR-accessible parameters that unambiguously determine the spatial arrangement of polypeptide chains. Inspired by work with cyclopeptides, model considerations showed that enforcing short non-bonding interatomic distances imposes «ring closure conditions» on polypeptide chains. Given that distances are scalar parameters, this indicated an avenue for studies of proteins in solution, i.e., under the regime of stochastic rotational and translational motions at frequencies in the nanosecond range (Brownian motion), where sharp pictures could not be obtained by photography-related methods. Later-on, we used distance geometry calculations with sets of inter-atomic distances derived from protein crystal structures to confirm that measurements of short proton-proton distances could provide atomic-resolution structures of globular proteins. During the years 1976-1984 the following four lines of research then led to protein structure determination by NMR in solution. First, the development of NMR experiments enabling the use of the nuclear Overhauser effect (NOE) for measurements of interatomic distances between pairs of hydrogen atoms in proteins. Second, obtaining sequence-specific resonance assignment solved the "phase problem" for protein structure determination by NMR. Third, generating and programming novel distance geometry algorithms enabled the calculation of atomic-resolution protein structures from limited sets of distance constraints measured by NMR. Fourth, the introduction of two-dimensional NMR provided greatly improved spectral resolution of the complex spectra of proteins as well as efficient delineation of scalar and dipole-dipole 1H-1H connectivities, thus making protein structure determination in solution viable and attractive.
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Affiliation(s)
- Kurt Wüthrich
- ETH Zürich, Zürich Switzerland and Scripps Research, La Jolla, CA, USA
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Rotating-Frame Overhauser Transfer via Long-Lived Coherences. Symmetry (Basel) 2021. [DOI: 10.3390/sym13091685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Solution-state distance restraints for protein structure determination with Ångström-level resolution rely on through-space transfer of magnetization between nuclear spins. Such magnetization transfers, named Overhauser effects, occur via dipolar magnetic couplings. We demonstrate improvements in magnetization transfer using long-lived coherences (LLCs)—singlet-triplet superpositions that are antisymmetric with respect to spin-permutation within pairs of coupled magnetic nuclei—as the magnetization source. Magnetization transfers in the presence of radio-frequency irradiation, known as ‘rotating-frame’ Overhauser effects (ROEs), are predicted by theory to improve by the use of LLCs; calculations are matched by preliminary experiments herein. The LLC-ROE transfers were compared to the transmission of magnetization via classical transverse routes. Long-lived coherences accumulate magnetization on an external third proton, K, with transfer rates that depended on the tumbling regime. I,S →K transfers in the LLC configuration for (I,S) are anticipated to match, and then overcome, the same transfer rates in the classical configuration as the molecular rotational correlation times increase. Experimentally, we measured the LLC-ROE transfer in dipeptide AlaGly between aliphatic protons in different residues K = Ala − Hα and (I,S) = Gly − Hα1,2 over a distance dK,I,S = 2.3 Å. Based on spin dynamics calculations, we anticipate that, for such distances, a superior transfer of magnetization occurs using LLC-ROE compared to classical ROE at correlation times above τC=10 ns. The LLC-ROE effect shows potential for improving structural studies of large proteins and offering constraints of increased precision for high-affinity protein-ligand complexes in slow tumbling in the liquid state.
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Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1. Biochim Biophys Acta Gen Subj 2021; 1865:129989. [PMID: 34389467 DOI: 10.1016/j.bbagen.2021.129989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we describe a new class of cryptides (peptides encrypted within a larger protein) with antimicrobial properties, named schistocins, derived from SmKI-1, a key protein in Shistosoma mansoni survival. This is a multi-functional protein with biotechnological potential usage as a therapeutic molecule in inflammatory diseases and to control schistosomiasis. METHODS We used our algorithm enCrypted, to perform an in silico proteolysis of SmKI-1 and a screening for potential antimicrobial activity. The selected peptides were chemically synthesized, tested in vitro and evaluated by both structural (CD, NMR) and biophysical (ITC) studies to access their structure-function relationship. RESULTS EnCrypted was capable of predicting AMPs in SmKI-1. Our biophysical analyses described a membrane-induced conformational change from random coil-to-α-helix and a peptide-membrane equilibrium for all schistocins. Our structural data allowed us to suggest a well-known mode of peptide-membrane interaction in which electrostatic attraction between the cationic peptides and anionic membranes results in the bilayer disordering. Moreover, the NMR exchange H/D data with the higher entropic contribution observed for the peptide-membrane interaction showed that shistocins have different orientations upon the membrane. CONCLUSIONS This work demonstrate the robustness for using the physicochemical features of predicted peptides in the identification of new bioactive cryptides besides the relevance of combining these analyses with biophysical methods to understand the peptide-membrane affinity and improve further algorithms. GENERAL SIGNIFICANCE Bioprospecting cryptides can be conducted through data mining of protein databases demonstrating the success of our strategy. The peptides-based agents derived from SmKI-1 might have high impact for system-biology and biotechnology.
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Russo L, Mascanzoni F, Farina B, Dolga AM, Monti A, Caporale A, Culmsee C, Fattorusso R, Ruvo M, Doti N. Design, Optimization, and Structural Characterization of an Apoptosis-Inducing Factor Peptide Targeting Human Cyclophilin A to Inhibit Apoptosis Inducing Factor-Mediated Cell Death. J Med Chem 2021; 64:11445-11459. [PMID: 34338510 DOI: 10.1021/acs.jmedchem.1c00777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Blocking the interaction between the apoptosis-inducing factor (AIF) and cyclophilin A (CypA) by the AIF fragment AIF(370-394) is protective against glutamate-induced neuronal cell death and brain injury in mice. Starting from AIF(370-394), we report the generation of the disulfide-bridged and shorter variant AIF(381-389) and its structural characterization by nuclear magnetic resonance (NMR) in the free and CypA-bound state. AIF(381-389) in both the free and bound states assumes a β-hairpin conformation similar to that of the fragment in the AIF protein and shows a highly reduced conformational flexibility. This peptide displays a similar in vitro affinity for CypA, an improved antiapoptotic activity in cells and an enhanced proteolytic stability compared to the parent peptide. The NMR-based 3D model of the AIF(381-389)/CypA complex provides a better understanding of the binding hot spots on both the peptide and the protein and can be exploited to design AIF/CypA inhibitors with improved pharmacokinetic and pharmacodynamics features.
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "L. Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Fabiola Mascanzoni
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Biancamaria Farina
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Amalia Mihaela Dolga
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, 35043 Marburg, Germany.,Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), Research School of Behavioural and Cognitive Neurosciences (BCN), Department of Molecular Pharmacology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Carsten Culmsee
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, 35043 Marburg, Germany
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "L. Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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Structure of Nanobody Nb23. Molecules 2021; 26:molecules26123567. [PMID: 34207949 PMCID: PMC8230604 DOI: 10.3390/molecules26123567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.
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