1
|
Adriana M, Aleksandra M, Denise B, Kinga G, Joanna W, Aleksandra H, Robert W, Agnieszka MW, Magdalena RŻ. Zn(II) and Cu(II) Coordination Enhances the Antimicrobial Activity of Piscidin 3, but Not That of Piscidins 1 and 2. Inorg Chem 2024; 63:12958-12968. [PMID: 38946498 PMCID: PMC11256756 DOI: 10.1021/acs.inorgchem.4c01659] [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] [Received: 04/23/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Piscidins, antimicrobial peptides isolated from fish, are potent against a variety of human pathogens; they show minimum inhibitory concentration values comparable to those of commercially used antimicrobials. Piscidins 1 and 2 are generally more effective than piscidin 3 when applied alone; the contrary is observed for their metal complexes: Zn(II) and Cu(II) coordination does not enhance the efficacy of piscidins 1 and 2, while a moderate enhancement is observed for piscidin 3. All three piscidins bind Cu(II) in a so-called albumin-like binding mode, while for Zn(II) complexes, two coordination modes are observed: piscidins 1 and 2 bind Zn(II) by imidazole nitrogens from His4, His11, and His17 side chains; piscidin 3 coordinates Zn(II) by His3, His4, and His11 imidazole nitrogens and additionally supports the interaction, formed by carbonyl oxygen from His4. Most likely, the high antimicrobial activity of piscidin complexes is due to neither the stability of their complexes nor the change in their secondary structure. Copper(II) complexes with piscidins 1 and 2 can form hydroxyl radicals, which could be responsible for the antimicrobial membrane damaging activity of these complexes. Clearly, a different mechanism (most likely an intercellular targeted one) is observed for piscidin 3 metal complexes; in most cases, the coordination of Cu(II) and Zn(II) enhances the antimicrobial potency of piscidin 3, showing that not only piscidin 3 alone but also its metal complexes have a different mode of action than piscidins 1 and 2.
Collapse
Affiliation(s)
- Miller Adriana
- Faculty
of Chemistry, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Mikołajczyk Aleksandra
- Screening
of Biological Activity Assays and Collection of Biological Material
Laboratory, Wroclaw Medical University Biobank, Faculty of Pharmacy, Wroclaw Medical University, ul. Borowska 211a, 50-556 Wroclaw, Poland
| | - Bellotti Denise
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Garstka Kinga
- Faculty
of Chemistry, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Wątły Joanna
- Faculty
of Chemistry, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Hecel Aleksandra
- Faculty
of Chemistry, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Wieczorek Robert
- Faculty
of Chemistry, University of Wroclaw, ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Matera-Witkiewicz Agnieszka
- Screening
of Biological Activity Assays and Collection of Biological Material
Laboratory, Wroclaw Medical University Biobank, Faculty of Pharmacy, Wroclaw Medical University, ul. Borowska 211a, 50-556 Wroclaw, Poland
| | | |
Collapse
|
2
|
Szarszoń K, Mikołajczyk A, Grelich-Mucha M, Wieczorek R, Matera-Witkiewicz A, Olesiak-Bańska J, Rowińska-Żyrek M, Wątły J. Bioinorganic chemistry of shepherin II complexes helps to fight Candida albicans? J Inorg Biochem 2024; 253:112476. [PMID: 38171045 DOI: 10.1016/j.jinorgbio.2023.112476] [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: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
The fungal cell wall and cell membrane are an important target for antifungal therapies, and a needle-like cell wall or membrane disruption may be an entirely novel antifungal mode of action. In this work, we show how the coordination of Zn(II) triggers the antifungal properties of shepherin II, a glycine- and histidine-rich antimicrobial peptide from the root of Capsella bursa-pastoris. We analyze Cu(II) and Zn(II) complexes of this peptide using experimental and theoretical methods, such as: mass spectrometry, potentiometry, UV-Vis and CD spectroscopies, AFM imaging, biological activity tests and DFT calculations in order to understand the correlation between their metal binding mode, structure, morphology and biological activity. We observe that Zn(II) coordinates to Shep II and causes a structural change, resulting in fibril formation, what has a pronounced biological consequence - a strong anticandidal activity. This phenomenon was observed neither for the peptide itself, nor for its copper(II) complex. The Zn(II) - shepherin II complex can be considered as a starting point for further anticandidal drug discovery, which is extremely important in the era of increasing antifungal drug resistance.
Collapse
Affiliation(s)
- Klaudia Szarszoń
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aleksandra Mikołajczyk
- Screening of Biological Activity Assays and Collection of Biological Material Laboratory, Wrocław Medical University Biobank, Faculty of Pharmacy, Wrocław Medical University, 50-556 Wrocław, Poland
| | - Manuela Grelich-Mucha
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Agnieszka Matera-Witkiewicz
- Screening of Biological Activity Assays and Collection of Biological Material Laboratory, Wrocław Medical University Biobank, Faculty of Pharmacy, Wrocław Medical University, 50-556 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | | - Joanna Wątły
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| |
Collapse
|
3
|
Kijewska M, Wołczański G, Kosson P, Wieczorek R, Lisowski M, Stefanowicz P. Stapling of leu-enkephalin analogs with bifunctional reagents for prolonged analgesic activity. Chem Commun (Camb) 2024; 60:3023-3026. [PMID: 38356394 DOI: 10.1039/d3cc06345c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The design and synthesis of leu-enkephalin analogs by replacing the glycine residues with N-(2-thioethyl)glycines and opening the cyclisation potential is presented. The cyclization (stapling) was achieved using bifunctional reagents (hexafluorobenzene and trithiocyanuric acid derivatives). The CD conformational studies of the stapled analogs suggest that the peptides adopt the type I β-turn conformation, which is in agreement with the theoretical analysis. The analog containing a trithiocyanuric acid derivative with a benzyl substituent shows potent analgesic activity.
Collapse
Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Grzegorz Wołczański
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Piotr Kosson
- Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warszawa, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Marek Lisowski
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| |
Collapse
|
4
|
Wyrzykowski D, Wieczorek R, Kloska A, Errante F, Papini AM, Makowska J. Influence of the modification of the cosmetic peptide Argireline on the affinity toward copper(II) ions. J Pept Sci 2024; 30:e3547. [PMID: 37752675 DOI: 10.1002/psc.3547] [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: 07/26/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023]
Abstract
Argireline (Ac-EEMQRR-NH2 ), a well-known neurotransmitter peptide with a potency similar to botulinum neurotoxins, reveals a proven affinity toward Cu(II) ions. We report herein Cu(II) chelating properties of three new Argireline derivatives, namely, AN4 (Ac-EAHRR-NH2 ), AN5 (Ac-EEHQRR-NH2 ), and AN6 (Ac-EAHQRK-NH2 ). Two complementary experimental techniques, i.e., potentiometric titration (PT) and isothermal titration calorimetry (ITC), have been employed to describe the acid-base properties of the investigated peptides as well as the thermodynamic parameters of the Cu(II) complex formation. Additionally, based on density functional theory (DFT) calculations, we propose the most likely structures of the resulting Cu-peptide complexes. Finally, the cytotoxicity of the free peptides and the corresponding Cu(II) complexes was estimated in human skin cells for their possible future cosmetic application. The biological results were subsequently compared with free Argireline, its Cu(II)-complexes, and the previously studied AN2 derivative (EAHQRR).
Collapse
Affiliation(s)
| | | | - Anna Kloska
- Faculty of Biology, Department of Medical Biology and Genetics, University of Gdańsk, Gdańsk, Poland
| | - Fosca Errante
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Neurofarba, University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | | |
Collapse
|
5
|
Stokowa-Sołtys K, Kierpiec K, Szczerba K, Wieczorek R. Can bacteria F. nucleatum be actively involved in colon cancer progression via a radical mediated mechanism? J Inorg Biochem 2023; 246:112307. [PMID: 37406386 DOI: 10.1016/j.jinorgbio.2023.112307] [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: 04/25/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Outer membrane proteins of Fusobacterium nucleatum, a cancer‑leading bacteria, are considered as the factors responsible for its pathogenicity. Among them, homotrimeric autotransporter protein YadA (Yersinia adhesin A) is an important virulence factor also found in the outer membrane of pathogenic Yersinia species. In this paper, the structure and stability of certain Cu(II) complexes with YadA fragments were investigated using both, experimental and theoretical methods. Potentiometry, UV-Vis, CD, EPR, and calculations at the density functional theory (DFT) level were applied to determine the metal ion coordination sphere. Moreover, the complexes ability to DNA cleavage and reactive oxygen species (ROS) production was studied. We have shown that copper(II) complexes can cleave DNA by 1O2, O2•- and •OH, which are formed in the studied systems. However, the results of electrophoretic experiments revealed that complexes cleave DNA less effectively than free copper(II) ions. Therefore, the presence of studied peptides may prevent DNA from a Cu(II)-induced damage to some extent.
Collapse
Affiliation(s)
- Kamila Stokowa-Sołtys
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
| | - Karolina Kierpiec
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Klaudia Szczerba
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| |
Collapse
|
6
|
Rola A, Potok P, Wieczorek R, Mos M, Gumienna-Kontecka E, Potocki S. Coordination Properties of the Zinc Domains of BigR4 and SmtB Proteins in Nickel Systems─Designation of Key Donors. Inorg Chem 2022; 61:9454-9468. [PMID: 35696675 PMCID: PMC9241078 DOI: 10.1021/acs.inorgchem.2c00319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The increasing number
of antibiotic-resistant pathogens has become
one of the foremost health problems of modern times. One of the most
lethal and multidrug-resistant bacteria is Mycobacterium
tuberculosis (Mtb), which causes tuberculosis (TB).
TB continues to engulf health systems due to the significant development
of bacterial multidrug-resistant strains. Mammalian immune system
response to mycobacterial infection includes, but is not limited to,
increasing the concentration of zinc(II) and other divalent metal
ions in phagosome vesicles up to toxic levels. Metal ions are necessary
for the survival and virulence of bacteria but can be highly toxic
to organisms if their concentrations are not strictly controlled.
Therefore, understanding the mechanisms of how bacteria use metal
ions to maintain their optimum concentrations and survive under lethal
environmental conditions is essential. The mycobacterial SmtB protein,
one of the metal-dependent transcription regulators of the ArsR/SmtB
family, dissociates from DNA in the presence of high concentrations
of metals, activating the expression of metal efflux proteins. In
this work, we explore the properties of α5 metal-binding domains
of SmtB/BigR4 proteins (the latter being the SmtB homolog from nonpathogenic Mycobacterium smegmatis), and two mutants of BigR4
as ligands for nickel(II) ions. The study focuses on the specificity
of metal–ligand interactions and describes the effect of mutations
on the coordination properties of the studied systems. The results
of this research reveal that the Ni(II)-BigR4 α5 species are
more stable than the Ni(II)-SmtB α5 complexes. His mutations,
exchanging one of the histidines for alanine, cause a decrease in
the stability of Ni(II) complexes. Surprisingly, the lack of His102
resulted also in increased involvement of acidic amino acids in the
coordination. The results of this study may help to understand the
role of critical mycobacterial virulence factor—SmtB in metal
homeostasis. Although SmtB prefers Zn(II) binding, it may also bind
metal ions that prefer other coordination modes, for example, Ni(II).
We characterized the properties of such complexes in order to understand
the nature of mycobacterial SmtB when acting as a ligand for metal
ions, given that nickel and zinc ArsR family proteins possess analogous
metal-binding motifs. This may provide an introduction to the design
of a new antimicrobial strategy against the pathogenic bacterium M. tuberculosis. The
histidine-rich α5 domains of SmtB (L4, Mycobacterium
tuberculosis) and BigR4 (L1, Mycobacterium
smegmatis) were studied as ligands
for Ni(II). Point mutation analysis of L1 revealed that His102 and
106 preferably bind metal ions. The general Ni(II)-binding motif for
both of the ligands was established as HX3HX3DX3HX2ED. L1 forms more
stable complexes than L4 due to the stabilizing effect of arginine
residues.
Collapse
Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Paulina Potok
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Magdalena Mos
- WMG, International Manufacturing Centre, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| |
Collapse
|
7
|
Stokowa-Soltys K, Kierpiec K, Wieczorek R. May Cu(II) binding, DNA cleavage and radicals production by YadA fragments be involved in the promotion of F. nucleatum related cancers? Dalton Trans 2022; 51:7040-7052. [DOI: 10.1039/d2dt00328g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In many cases, human microbiota is associated with cancer progression. It was concluded that Fusobacterium nucleatum increases neoplastic changes. This bacterium is naturally present in the human dental plaque. However,...
Collapse
|
8
|
Stokowa-Sołtys K, Wojtkowiak K, Dzyhovskyi V, Wieczorek R. Effect of Copper(II) Ion Binding by Porin P1 Precursor Fragments from Fusobacterium nucleatum on DNA Degradation. Int J Mol Sci 2021; 22:ijms222212541. [PMID: 34830424 PMCID: PMC8623562 DOI: 10.3390/ijms222212541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
Fusobacterium nucleatum is one of the most notorious species involved in colorectal cancer. It was reported that numerous outer membrane proteins (OMP) are actively involved in carcinogenesis. In this paper, the structure and stability of certain complexes, as well as DNA cleavage and ROS generation by fragments of OMP, were investigated using experimental and theoretical methods. Mass spectrometry, potentiometry, UV-Vis, CD, EPR, gel electrophoresis and calculations at the density functional theory (DFT) level were applied. Two consecutive model peptides, Ac-AKGHEHQLE-NH2 and Ac-FGEHEHGRD-NH2, were studied. Both of these were rendered to form a variety of thermodynamically stable complexes with copper(II) ions. All of the complexes were stabilized, mainly due to interactions of metal with nitrogen and oxygen donor atoms, as well as rich hydrogen bond networks. It was also concluded that these complexes in the presence of hydrogen peroxide or ascorbic acid can effectively produce hydroxyl radicals and have an ability to cleave the DNA strands. Surprisingly, the second studied ligand at the micromolar concentration range causes overall DNA degradation.
Collapse
|
9
|
Żamojć K, Wyrzykowski D, Sabatino G, Papini AM, Wieczorek R, Chmurzyński L, Makowska J. Key role of histidine residues orientation in affinity binding of model pentapeptides with Ni2+ ions: A theoretical supported experimental study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
10
|
A Non-Covalent Dimer Formation of Quaternary Ammonium Cation with Unusual Charge Neutralization in Electrospray-Ionization Mass Spectrometry. Molecules 2021; 26:molecules26195868. [PMID: 34641412 PMCID: PMC8511985 DOI: 10.3390/molecules26195868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 11/25/2022] Open
Abstract
Specific and nonspecific non-covalent molecular association of biomolecules is characteristic for electrospray-ionization mass spectrometry analysis of biomolecules. Understanding the interaction between two associated molecules is of significance not only from the biological point of view but also gas phase analysis by mass spectrometry. Here we reported a formation of non-covalent dimer of quaternary ammonium denatonium cation with +1 charge detected in the positive ion mode electrospray ionization mass spectrometry analysis of denatonium benzoate. Hydrogen deuterium exchange of amide and carbon-bonded hydrogens revealed that charge neutralization of one denatonium cation is the consequence of amide hydrogen dissociation. DFT (Density Functional Theory) calculations proved high thermodynamic stable of formed dimer stabilized by the short and strong N..H-N hydrogen bond. The signal intensity of the peak characterizing non-covalent dimer is low intensity and does not depend on the sample concentration. Additionally, dimer observation was found to be instrument-dependent. The current investigation is the first experimental and theoretical study on the quaternary ammonium ions dimer. Thus the present study has great significance for understanding the structures of the biomolecules as well as materials.
Collapse
|
11
|
Bąchor U, Drozd-Szczygieł E, Bąchor R, Jerzykiewicz L, Wieczorek R, Mączyński M. New water-soluble isoxazole-linked 1,3,4-oxadiazole derivative with delocalized positive charge. RSC Adv 2021; 11:29668-29674. [PMID: 35479548 PMCID: PMC9040910 DOI: 10.1039/d1ra05116d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022] Open
Abstract
Herein we present a synthesis and characterization of a new and unique low-weight heterocyclic compound 5-amino-2-(5-amino-3-methyl-1,2-oxazol-4-yl)-3-methyl-2,3-dihydro-1,3,4-oxadiazol-2-ylium bromide with the unusual electron charge delocalization owing the local positive charge at the carbon atom of oxadiazole moiety. X-ray single crystal of C7H10N5O2·Br- showed the molecule crystalized in monoclinic, space group P21/c. Both five membered rings are planar and twisted forming the ring motif with the counter ion where H⋯Br interactions are one of the dominant. The presented compound is characterized by high ionization efficiency in ESI-MS mode and undergoes dissociation within oxadiazole moiety under ESI-MS/MS conditions even under low collision energies. The presented compound is an interesting example of heterocyclic stable carbocation which may serve as a new lead structure.
Collapse
Affiliation(s)
- Urszula Bąchor
- Department of Organic Chemistry, Faculty of Pharmacy, Wroclaw Medical University Borowska 211A 50-556 Wroclaw Poland
| | - Ewa Drozd-Szczygieł
- Department of Organic Chemistry, Faculty of Pharmacy, Wroclaw Medical University Borowska 211A 50-556 Wroclaw Poland
| | - Remigiusz Bąchor
- Faculty of Chemistry, University of Wroclaw F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Lucjan Jerzykiewicz
- Faculty of Chemistry, University of Wroclaw F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Marcin Mączyński
- Department of Organic Chemistry, Faculty of Pharmacy, Wroclaw Medical University Borowska 211A 50-556 Wroclaw Poland
| |
Collapse
|
12
|
Rola A, Wieczorek R, Kozłowski H, Krzywoszyńska K, Potocki S. Sometimes less is more-the impact of the number of His residues on the stability of Zn(II)-SmtB and BigR4 α-5 domain complexes. Dalton Trans 2021; 50:12118-12129. [PMID: 34388229 DOI: 10.1039/d1dt01690c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The increasing number of antibiotic-resistant pathogens has become one of the major health problems of modern times, including infections caused by Mycobacterium tuberculosis. One of the possible mammalian immune system responses to mycobacterial infection is the increase of the zinc(ii) concentration in phagosomes to a toxic level. The mycobacterial SmtB protein belongs to the family of ArsR/SmtB transcription regulators. In the presence of high concentrations of metals, SmtB dissociates from DNA and activates the expression of metal efflux proteins. In this work, we focus on the α5 zinc(ii) binding domains of SmtB/BigR4 proteins (the latter being the SmtB homolog from non-pathogenic M. smegmatis) and two mutants of BigR4. We will be taking a closer look at the coordination modes and thermodynamic properties of their zinc(ii) complexes. The study points out the specificity of metal-ligand interactions and describes the effect of mutations on the coordination properties of the studied systems. The stabilities of the zinc(ii) complexes were determined by potentiometry. The coordination sites were determined by NMR experiments and DFT calculations. The comparison of complex stabilities reveals that the Zn(ii)-BigR4 species are more stable than the Zn(ii)-SmtB complexes. His mutations strongly affect the stability of the complexes and the coordination modes of the metal ion. Exchanging one of the histidines for alanine causes, surprisingly, an increase in the stability of zinc(ii) complexes with the studied domain. This was confirmed by potentiometric and DFT methods. This work can be considered as a bioinorganic introduction to the discovery of new strategies in M. tuberculosis infection treatment based on zinc(ii)-sensitive mechanisms.
Collapse
Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 St, 50-383 Wroclaw, Poland.
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 St, 50-383 Wroclaw, Poland.
| | - Henryk Kozłowski
- Institute of Health Sciences, University of Opole, Katowicka 68 St, 45-060 Opole, Poland
| | - Karolina Krzywoszyńska
- Institute of Health Sciences, University of Opole, Katowicka 68 St, 45-060 Opole, Poland
| | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 St, 50-383 Wroclaw, Poland.
| |
Collapse
|
13
|
Kędziora A, Wieczorek R, Speruda M, Matolínová I, Goszczyński TM, Litwin I, Matolín V, Bugla-Płoskońska G. Comparison of Antibacterial Mode of Action of Silver Ions and Silver Nanoformulations With Different Physico-Chemical Properties: Experimental and Computational Studies. Front Microbiol 2021; 12:659614. [PMID: 34276595 PMCID: PMC8281304 DOI: 10.3389/fmicb.2021.659614] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/02/2021] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to compare the antibacterial mode of action of silver ions (Ag+) and selected silver nanoformulations against E. coli strains (E. coli J53, Escherichia coli BW25113 and its derivatives: Δ ompA, Δ ompC, Δ ompF, Δ ompR, ompRG596AcusSG1130A, cusSG1130A). In this research we used various experimental methods and techniques such as determination of the minimal inhibitory concentration, flow cytometry, scanning electron microscopy, circular dichroism as well as computational methods of theoretical chemistry. Thanks to the processing of bacteria and silver samples (ions and nanoformulations), we were able to determine the bacterial sensitivity to silver samples, detect reactive oxygen species (ROS) in the bacterial cells, visualize the interaction of silver samples with the bacterial cells, and identify their interactions with proteins. Differences between the mode of action of silver ions and nanoformulations and the action of nanoformulations themselves were revealed. Based on the results of computational methods, we proposed an explanation of the differences in silver-outer protein interaction between silver ions and metallic silver; in general, the Ag0 complexes exhibit weaker interaction than Ag+ ones. Moreover, we identified two gutter-like areas of the inner layer of the ion channel: one more effective, with oxygen-rich side chains; and another one less effective, with nitrogen-rich side chains.
Collapse
Affiliation(s)
- Anna Kędziora
- Department of Microbiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | | | - Mateusz Speruda
- Department of Microbiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Iva Matolínová
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Tomasz M Goszczyński
- Laboratory of Biomedical Chemistry, Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, PAS, Wrocław, Poland
| | - Ireneusz Litwin
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Vladimír Matolín
- Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | | |
Collapse
|
14
|
Stokowa-Sołtys K, Dzyhovskyi V, Wieczorek R, Jeżowska-Bojczuk M. Coordination pattern and reactivity of two model peptides from porin protein P1. J Inorg Biochem 2020; 215:111332. [PMID: 33340803 DOI: 10.1016/j.jinorgbio.2020.111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022]
Abstract
It has been reported that numerous of Fusobacterium nucleatum outer membrane proteins take part in cancerogenesis. Therefore, it is very interesting to study their interactions with metal ions and the ability to produce reactive oxygen species, which may be involved in cancer progression. Since investigations of metal binding to proteins are often based on fragments that contain the metal-binding domains, designing model peptides should be very mindful. As was shown in this paper, very similar protein fragments may behave differentially. Herein, combined potentiometric, spectroscopic, and computational studies were performed to determine metal ion binding by ligands constituting fragments of porin protein P1. Two studied tetrapeptides (Ac-KEHK-NH2 and Ac-EHKA-NH2) that have common EHK motif have different coordination properties and reactivity. Therefore, we should be cautious when transferring the behavior of small peptide fragments to whole protein.
Collapse
Affiliation(s)
- Kamila Stokowa-Sołtys
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
| | - Valentyn Dzyhovskyi
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | | |
Collapse
|
15
|
On the acid-base properties of pyrazine-2-thiocarboxamide and its complexes with Fe(II), Cu(II), Zn(II) and Ni(II) in polar solvents. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
16
|
Wątły J, Hecel A, Wieczorek R, Swiątek-Kozłowska J, Kozłowski H, Rowińska-Żyrek M. Uncapping the N-terminus of a ubiquitous His-tag peptide enhances its Cu 2+ binding affinity. Dalton Trans 2019; 48:13567-13579. [PMID: 31309219 DOI: 10.1039/c9dt01635j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal complexes with an N-terminally free and N-terminally acetylated polyhistidine region of Echis ocellatus venom, with an interesting His-rich motif present in numerous metal binding proteins from all kingdoms of life (DHDHDHHHHHHPGSSV-NH2 and Ac-DHDHDHHHHHHPGSSV-NH2) show the role of the free amino group in the thermodynamic enhancement of Cu2+, Ni2+ and Zn2+ binding. In the studied sequences, Cu2+ can be coordinated by different sets of imidazole rings, and a 3-10 helix is detected in close proximity of Cu2+ binding sites. The complexes are more stable than those with a typical His6-tag, despite a similar copper(ii) coordination mode in both cases.
Collapse
Affiliation(s)
- J Wątły
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50383, Wroclaw, Poland.
| | | | | | | | | | | |
Collapse
|
17
|
Carnahan SL, Lampkin BJ, Naik P, Hanrahan MP, Slowing II, VanVeller B, Wu G, Rossini AJ. Probing O–H Bonding through Proton Detected 1H–17O Double Resonance Solid-State NMR Spectroscopy. J Am Chem Soc 2018; 141:441-450. [DOI: 10.1021/jacs.8b10878] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Scott L. Carnahan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Bryan J. Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Pranjali Naik
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Michael P. Hanrahan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Igor I. Slowing
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Gang Wu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Aaron J. Rossini
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| |
Collapse
|
18
|
Brasili D, Watly J, Simonovsky E, Guerrini R, Barbosa NA, Wieczorek R, Remelli M, Kozlowski H, Miller Y. The unusual metal ion binding ability of histidyl tags and their mutated derivatives. Dalton Trans 2016; 45:5629-39. [DOI: 10.1039/c5dt04747a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptides that consist of repeated sequences of alternating histidines and alanines strongly bind Cu(ii) and form α-helical structures.
Collapse
Affiliation(s)
- Davide Brasili
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Joanna Watly
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Eyal Simonovsky
- Department of Chemistry
- Ben Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Nuno A. Barbosa
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Robert Wieczorek
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Maurizio Remelli
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Henryk Kozlowski
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Yifat Miller
- Department of Chemistry
- Ben Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| |
Collapse
|
19
|
Kauch M, Pecul M. What factors influence the metal-proton spin-spin coupling constants in mercury- and cadmium-substutited rubredoxin? J Phys Chem A 2014; 118:4471-9. [PMID: 24884758 DOI: 10.1021/jp501888c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The indirect metal-proton spin-spin coupling constants between protons in cysteine groups and the mercury or cadmium nucleus have been calculated for a small model of Me-rubredoxin complex (Me = Cd, Hg) by means of density functional theory with zeroth-order regular approximation Hamiltonian (DFT-ZORA). The calculated spin-spin coupling constants, in spite of the moderate size of the model system, are in good agreement with the values measured in NMR experiment, which are in the 0.29-0.56 Hz range for the Cd complex and in the 0.57-2.20 Hz range for the Hg complex. The robustness of the chosen method has been verified by calculations with a number of different exchange-correlation functionals and basis sets. Additionally, it has been shown that the short- and long-distance metal-proton coupling constants are affected mainly by the values of the metal-proton distance and the H-N-C-C dihedral angle.
Collapse
Affiliation(s)
- Małgorzata Kauch
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warszawa, Poland
| | | |
Collapse
|
20
|
Pohl G, Asensio A, Dannenberg JJ. Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study. Biochemistry 2014; 53:617-23. [PMID: 24422496 PMCID: PMC3985835 DOI: 10.1021/bi401366w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.
Collapse
Affiliation(s)
- Gabor Pohl
- Department of Chemistry, City University of New York, Hunter College and the Graduate School , 695 Park Avenue, New York, New York 10065, United States
| | | | | |
Collapse
|
21
|
Chiera NM, Rowinska-Zyrek M, Wieczorek R, Guerrini R, Witkowska D, Remelli M, Kozlowski H. Unexpected impact of the number of glutamine residues on metal complex stability. Metallomics 2013; 5:214-21. [DOI: 10.1039/c3mt20166j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
22
|
Plumley JA, Dannenberg JJ. A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error. J Comput Chem 2011; 32:1519-27. [PMID: 21328398 PMCID: PMC3073166 DOI: 10.1002/jcc.21729] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/07/2010] [Accepted: 11/09/2010] [Indexed: 11/07/2022]
Abstract
We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.
Collapse
Affiliation(s)
- Joshua A. Plumley
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
| | - J. J. Dannenberg
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
| |
Collapse
|
23
|
Olejniczak M, Pecul M. Spin-Spin Coupling Constants Transmitted through IrH⋅⋅⋅HN Dihydrogen Bonds. Chemphyschem 2009; 10:1247-59. [DOI: 10.1002/cphc.200800817] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
24
|
Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
Collapse
Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
| | | | | | | |
Collapse
|
25
|
Juranić N, Dannenberg JJ, Cornilescu G, Salvador P, Atanasova E, Ahn HC, Macura S, Markley JL, Prendergast FG. Structural dependencies of protein backbone 2JNC' couplings. Protein Sci 2008; 17:768-76. [PMID: 18305196 DOI: 10.1110/ps.073331608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone (2)J(NC') couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental (2)J(NC') couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated (2)J(NC') couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from (h3)J(NC') couplings, provides useful insight into the overall energy profile of the protein backbone in solution.
Collapse
Affiliation(s)
- Nenad Juranić
- Department of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | |
Collapse
|