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Kirschner H, John M, Zhou T, Bachmann N, Schultz A, Hofmann E, Bandow JE, Scherkenbeck J, Metzler-Nolte N, Stoll R. Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase. ChemMedChem 2024; 19:e202300538. [PMID: 38057137 DOI: 10.1002/cmdc.202300538] [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: 10/06/2023] [Revised: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The lack of new antibiotics and the rapidly rising number of pathogens resistant to antibiotics pose a serious problem to mankind. In bacteria, the cell membrane provides the first line of defence to antibiotics by preventing them from reaching their molecular target. To overcome this entrance barrier, it has been suggested[1] that small Gold-Nanoparticles (AuNP) could possibly function as drug delivery systems for antibiotic ligands. Using actinonin-based ligands, we provide here proof-of-principle of AuNP functionalisation, the capability to bind and inhibit the target protein of the ligand, and the possibility to selectively release the antimicrobial payload. To this end, we successfully synthesised AuNP coated with thio-functionalised actinonin and a derivative. Interactions between 15N-enriched His-peptide deformylase 1-147 from E. coli (His-ecPDF 1-147) and compound-coated AuNP were investigated via 2D 1H-15N-HSQC NMR spectra proving the direct binding to His-ecPDF 1-147. More importantly by adding dithiothreitol (DTT), we show that the derivative is successfully released from AuNPs while still bound to His-ecPDF 1-147. Our findings indicate that AuNP-conjugated ligands can address and bind intracellular target proteins. The system introduced here presents a new delivery platform for antibiotics and allows for the easy optimisation of ligand coated AuNPs.
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Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Milena John
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tianyi Zhou
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - André Schultz
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Jürgen Scherkenbeck
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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Lipiński PFJ, Garnuszek P, Maurin M, Stoll R, Metzler-Nolte N, Wodyński A, Dobrowolski JC, Dudek MK, Orzełowska M, Mikołajczak R. Structural studies on radiopharmaceutical DOTA-minigastrin analogue (CP04) complexes and their interaction with CCK2 receptor. EJNMMI Res 2018; 8:33. [PMID: 29663167 PMCID: PMC5902437 DOI: 10.1186/s13550-018-0387-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Background The cholecystokinin receptor subtype 2 (CCK-2R) is an important target for diagnostic imaging and targeted radionuclide therapy (TRNT) due to its overexpression in certain cancers (e.g., medullary thyroid carcinoma (MTC)), thus matching with a theranostic principle. Several peptide conjugates suitable for the TRNT of MTC have been synthesized, including a very promising minigastrin analogue DOTA-(DGlu)6-Ala-Tyr-Gly-Trp-Met-Asp-Phe-NH2 (CP04). In this contribution, we wanted to see whether CP04 binding affinity for CCK-2R is sensitive to the type of the complexed radiometal, as well as to get insights into the structure of CP04-CCK2R complex by molecular modeling. Results In vitro studies demonstrated that there is no significant difference in CCK-2R binding affinity and specific cellular uptake between the CP04 conjugates complexed with [68Ga]Ga3+ or [177Lu]Lu3+. In order to investigate the background of this observation, we proposed a binding model of CP04 with CCK-2R based on homology modeling and molecular docking. In this model, the C-terminal part of the molecule enters the cavity formed between the receptor helices, while the N-terminus (including DOTA and the metal) is located at the binding site outlet, exposed in large extent to the solvent. The radiometals do not influence the conformation of the molecule except for the direct neighborhood of the chelating moiety. Conclusions The model seems to be in agreement with much of structure-activity relationship (SAR) studies reported for cholecystokinin and for CCK-2R-targeting radiopharmaceuticals. It also explains relative insensitivity of CCK-2R affinity for the change of the metal. The proposed model partially fits the reported site-directed mutagenesis data.
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Affiliation(s)
- Piotr F J Lipiński
- Neuropeptides Department, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5 Str., 02-106, Warszawa, Poland.
| | - Piotr Garnuszek
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Michał Maurin
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Nils Metzler-Nolte
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Artur Wodyński
- Świerk Computing Centre, National Centre for Nuclear Research, A. Sołtana 7 Str., 05-400, Otwock, Poland.,Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, Dorodna 16 Street, 03-195, Warszawa, Poland.,National Medicines Institute, Chełmska 30/34 Str., 00-725, Warszawa, Poland
| | - Marta K Dudek
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Monika Orzełowska
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Renata Mikołajczak
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
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Markley JL, Westler WM. Biomolecular NMR: Past and future. Arch Biochem Biophys 2017; 628:3-16. [PMID: 28495511 PMCID: PMC5701516 DOI: 10.1016/j.abb.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 12/28/2022]
Abstract
The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR. What follows is our personal experience with the evolution of the field, which we hope will illustrate the trajectory of change over the years. As for the future, one can confidently predict that it will involve unexpected advances. Our narrative is colored by our experience in using the NMR Facility for Biomedical Studies at Carnegie-Mellon University (Pittsburgh) and in developing similar facilities at Purdue (1977-1984) and the University of Wisconsin-Madison (1984-). We have enjoyed developing NMR technology and making it available to collaborators and users of these facilities. Our group's association with the Biological Magnetic Resonance data Bank (BMRB) and with the Worldwide Protein Data Bank (wwPDB) has also been rewarding. Of course, many groups contributed to the early growth and development of biomolecular NMR, and our brief personal account certainly omits many important milestones.
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Affiliation(s)
- John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - William Milo Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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Probing multimodal ligand binding regions on ubiquitin using nuclear magnetic resonance, chromatography, and molecular dynamics simulations. J Chromatogr A 2012; 1229:113-20. [DOI: 10.1016/j.chroma.2011.12.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 11/15/2011] [Accepted: 12/23/2011] [Indexed: 11/23/2022]
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Kokoschka M, Bangert JA, Stoll R, Sheldrick WS. Sequence-Selective Organoiridium DNA Bis-Intercalators with Flexible Dithiaalkane Linker Chains. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.200901123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ali Nazif M, Bangert JA, Ott I, Gust R, Stoll R, Sheldrick WS. Dinuclear organoiridium(III) mono- and bis-intercalators with rigid bridging ligands: Synthesis, cytotoxicity and DNA binding. J Inorg Biochem 2009; 103:1405-14. [DOI: 10.1016/j.jinorgbio.2009.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/06/2009] [Accepted: 08/06/2009] [Indexed: 10/20/2022]
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Schrader N, Koerner C, Koessmeier K, Bangert JA, Wittinghofer A, Stoll R, Vetter IR. The crystal structure of the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex. Structure 2008; 16:1116-25. [PMID: 18611384 DOI: 10.1016/j.str.2008.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 03/14/2008] [Accepted: 03/22/2008] [Indexed: 10/21/2022]
Abstract
Nucleoporin (Nup) 153 is a highly mobile, multifunctional, and essential nuclear pore protein. It contains four zinc finger motifs that are thought to be crucial for the regulation of transport-receptor/cargo interactions via their binding to the small guanine nucleotide binding protein, Ran. We found this interaction to be independent of the phoshorylation state of the nucleotide. Ran binds with the highest affinity to the second zinc finger motif of Nup153 (Nup153ZnF2). Here we present the crystal structure of this complex, revealing a new type of Ran-Ran interaction partner interface together with the solution structure of Nup153ZnF2. According to our complex structure, Nup153ZnF2 binding to Ran excludes the formation of a Ran-importin-beta complex. This finding suggests a local Nup153-mediated Ran reservoir at the nucleoplasmic distal ring of the nuclear pore, where nucleotide exchange may take place in a ternary Nup153-Ran-RCC1 complex, so that import complexes are efficiently terminated.
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Affiliation(s)
- Nils Schrader
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Biochemical characterisation of TCTP questions its function as a guanine nucleotide exchange factor for Rheb. FEBS Lett 2008; 582:3005-10. [PMID: 18692051 DOI: 10.1016/j.febslet.2008.07.057] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/19/2008] [Accepted: 07/23/2008] [Indexed: 11/20/2022]
Abstract
Translationally controlled tumour protein (TCTP) is involved in malignant transformation and regulation of apoptosis. It has been postulated to serve as a guanine nucleotide exchange factor for the small G-protein Rheb. Rheb functions in the PI3 kinase/mTOR pathway. The study presented here was initiated to characterise the interaction between TCTP and Rheb biochemically. Since (i) no exchange activity of TCTP towards Rheb could be detected in vitro, (ii) no interaction between TCTP and Rheb could be detected by NMR spectroscopy, and (iii) no effect of TCTP depletion in cells on the direct downstream targets of Rheb could be observed in vivo, this study shows that TCTP is unlikely to be a guanine nucleotide exchange factor for Rheb.
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NMR evaluation of adipocyte fatty acid binding protein (aP2) with R- and S-ibuprofen. Bioorg Med Chem 2008; 16:4323-30. [DOI: 10.1016/j.bmc.2008.02.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2007] [Revised: 02/11/2008] [Accepted: 02/25/2008] [Indexed: 01/22/2023]
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Schumann FH, Riepl H, Maurer T, Gronwald W, Neidig KP, Kalbitzer HR. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions. JOURNAL OF BIOMOLECULAR NMR 2007; 39:275-89. [PMID: 17955183 DOI: 10.1007/s10858-007-9197-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 08/31/2007] [Indexed: 05/20/2023]
Abstract
Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation Deltadelta comb In this paper different procedures (published and non-published) to calculate Deltadelta comb are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data.
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Affiliation(s)
- Frank H Schumann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
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11
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Gáspári Z, Szenthe B, Patthy A, Westler WM, Gráf L, Perczel A. Local binding with globally distributed changes in a small protease inhibitor upon enzyme binding. FEBS J 2006; 273:1831-42. [PMID: 16623717 DOI: 10.1111/j.1742-4658.2006.05204.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Complexation of the small serine protease inhibitor Schistocerca gregaria chymotrypsin inhibitor (SGCI), a member of the pacifastin inhibitor family, with bovine chymotrypsin was followed by NMR spectroscopy. (1)H-(15)N correlation (HSQC) spectra of the inhibitor with increasing amounts of the enzyme reveal tight and specific binding in agreement with biochemical data. Unexpectedly, and unparalleled among canonical serine protease inhibitors, not only residues in the protease-binding loop of the inhibitor, but also some segments of it located spatially far from the substrate-binding cleft of the enzyme were affected by complexation. However, besides changes, some of the dynamical features of the free inhibitor are retained in the complex. Comparison of the free and complexed inhibitor structures revealed that most, but not all, of the observed chemical shift changes can be attributed to minor structural transitions. We suggest that the classical 'scaffold + binding loop' model of canonical inhibitors might not be fully valid for the inhibitor family studied. In our view, this feature allows for the emergence of both taxon-specific and nontaxon-specific inhibitors in this group of small proteins.
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Affiliation(s)
- Zoltán Gáspári
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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Abstract
With the amount of genetic information available, a lot of attention has focused on systems biology, in particular biomolecular interactions. Considering the huge number of such interactions, and their often weak and transient nature, conventional experimental methods such as X-ray crystallography and NMR spectroscopy are not sufficient to gain structural insight into these. A wealth of biochemical and/or biophysical data can, however, readily be obtained for biomolecular complexes. Combining these data with docking (the process of modeling the 3D structure of a complex from its known constituents) should provide valuable structural information and complement the classical structural methods. In this review we discuss and illustrate the various sources of data that can be used to map interactions and their combination with docking methods to generate structural models of the complexes. Finally a perspective on the future of this kind of approach is given.
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Affiliation(s)
- Aalt D J van Dijk
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, the Netherlands
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Rajabzadeh M, Kao J, Frieden C. Consequences of Single-Site Mutations in the Intestinal Fatty Acid Binding Protein. Biochemistry 2003; 42:12192-9. [PMID: 14567680 DOI: 10.1021/bi0301688] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intestinal fatty acid binding protein (IFABP) is a small (15 kDa) protein consisting mostly of 10 antiparallel beta-strands (A-J) and a small helical region that serves as a portal for the ligand. Two beta-sheet structures (strands A-E and F-J) surround a cavity into which the ligand binds. In this work, we investigated how changes in the side chains of specific residues are propagated through the structure. To determine what these changes were and how they relate to changes in stability, (15)N chemical shift perturbations were measured and compared to those of the wild-type protein. Seven mutations, five of which change either valine or leucine to glycine, have been examined. All these mutants were less stable than wild-type IFABP, suggesting some structural changes. For five of the mutants, the data suggest that destabilization of a small region of the protein propagates throughout the structure, resulting in an overall decrease in stability. In two (Leu38Gly and Leu89Gly), the loss of cooperativity in the equilibrium denaturation curves suggests that the destabilization of one region may not be transmitted to other regions in a cooperative manner. It is shown that the effect of mutating hydrophobic residues is much greater than that observed upon mutation of a solvent-exposed polar residue.
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Georgescu RE, Alexov EG, Gunner MR. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys J 2002; 83:1731-48. [PMID: 12324397 PMCID: PMC1302268 DOI: 10.1016/s0006-3495(02)73940-4] [Citation(s) in RCA: 378] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Protein stability and function relies on residues being in their appropriate ionization states at physiological pH. In situ residue pK(a)s also provides a sensitive measure of the local protein environment. Multiconformation continuum electrostatics (MCCE) combines continuum electrostatics and molecular mechanics force fields in Monte Carlo sampling to simultaneously calculate side chain ionization and conformation. The response of protein to charges is incorporated both in the protein dielectric constant (epsilon(prot)) of four and by explicit conformational changes. The pK(a) of 166 residues in 12 proteins was determined. The root mean square error is 0.83 pH units, and >90% have errors of <1 pH units whereas only 3% have errors >2 pH units. Similar results are found with crystal and solution structures, showing that the method's explicit conformational sampling reduces sensitivity to the initial structure. The outcome also changes little with protein dielectric constant (epsilon(prot) 4-20). Multiconformation continuum electrostatics titrations show coupling of conformational flexibility and changes in ionization state. Examples are provided where ionizable side chain position (protein G), Asn orientation (lysozyme), His tautomer distribution (RNase A), and phosphate ion binding (RNase A and H) change with pH. Disallowing these motions changes the calculated pK(a).
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