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Uddin IA, Stec E, Papadantonakis GA. Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs. Chemphyschem 2024; 25:e202300946. [PMID: 38381922 DOI: 10.1002/cphc.202300946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
Gas-phase and aqueous vertical ionization potentials, vIPgas and vIPaq respectively and measurements of the molecular electrostatic and local ionization maps calculated at the DFT/B3LYP-D3/ 6-311+G** level of theory and the C-PCM reaction field model for single- and double-stranded CpG and 5MeCpG pairs show that the vIPaq for single- and double-stranded pairs of C-G and 5MeC-G are practically the same, in the range of 5.79 to 5.81 eV. The aqueous adiabatic ionization potentials for single-stranded CpG and 5MeCpG are 5.52 eV and 5.51 eV respectively and they reflect the nuclear reorganization that takes place after the abstraction of the electron. The aqueous adiabatic ionization energy values that correspond to the CpG+. radical cation and the hydrated electron, e-,, being at infinite distance, adIPaq+Vo, are 3.92 eV and 3.91 eV respectively with (Vo=-1.6 eV) Analysis of data suggest that the HOMO-LUMO energy gap in the hard/soft-acid/base (HSAB) concept cannot be used a priori to determine the effect of cytosine methylation on the guanine enhanced oxidative damage in DNA.
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Affiliation(s)
- Ismihan A Uddin
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - Ewa Stec
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
| | - George A Papadantonakis
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL 60515
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Uddin IA, Stec E, Papadantonakis GA. Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs. Chemphyschem 2024; 25:e202400391. [PMID: 38712664 DOI: 10.1002/cphc.202400391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The front cover artwork is provided by Prof. Papadantonakis' group. The image shows a Watson-Crick Guanine-Cytosine pair, and the difference between vertical and adiabatic ionization potentials. Read the full text of the Research Article at 10.1002/cphc.202300946.
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Affiliation(s)
- Ismihan A Uddin
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL, 60515
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL, 60515
| | - Ewa Stec
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL, 60515
| | - George A Papadantonakis
- University of Illinois Chicago, Department of Chemistry, 845 W. Taylor St. Room 4506 SES, Chicago, IL. 60607
- Midwestern University Chicago, College of Osteopathic Medicine and formerly at University of Illinois Chicago, Department of Chemistry, 555 31st St., Downers Grove, IL, 60515
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Lombardi J, Stec E, Edwards M, Connell T, Sandor M. Comparison of mechanical properties and host tissue response to OviTex™ and Strattice™ surgical meshes: author reply. Hernia 2024; 28:281-282. [PMID: 37855939 PMCID: PMC10891220 DOI: 10.1007/s10029-023-02911-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/01/2023] [Indexed: 10/20/2023]
Affiliation(s)
- J Lombardi
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - E Stec
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - M Edwards
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - T Connell
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - M Sandor
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA.
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Lombardi J, Stec E, Edwards M, Connell T, Sandor M. Comparison of mechanical properties and host tissue response to OviTex™ and Strattice™ surgical meshes. Hernia 2023; 27:987-997. [PMID: 37031315 PMCID: PMC10374700 DOI: 10.1007/s10029-023-02769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/01/2023] [Indexed: 04/10/2023]
Abstract
PURPOSE This study compared the in vitro/benchtop and in vivo mechanical properties and host biologic response to ovine rumen-derived/polymer mesh hybrid OviTex™ with porcine-derived acellular dermal matrix Strattice™ Firm. METHODS OviTex 2S Resorbable (OviTex 2S-R) and Strattice morphology were examined in vitro using histology and scanning electron microscopy; mechanical properties were assessed via tensile test; in vivo host biologic response and explant mechanics were evaluated in a rodent subcutaneous model. Separately, OviTex 1S Permanent (OviTex 1S-P) and Strattice were evaluated in a primate abdominal wall repair model. RESULTS OviTex 2S-R demonstrated layer separation, whereas Strattice retained its structural integrity and demonstrated higher maximum load than OviTex 2S-R out-of-package (124.8 ± 11.1 N/cm vs 37.9 ± 5.5 N/cm, p < 0.001), 24 h (55.7 ± 7.4 N/cm vs 5.6 ± 3.8 N/cm, p < 0.001), 48 h (45.3 ± 14.8 N/cm vs 2.8 ± 2.6 N/cm, p = 0.003), and 72 h (29.2 ± 10.5 N/cm vs 3.2 ± 3.1 N/cm, p = 0.006) following collagenase digestion. In rodents, inflammatory cell infiltration was observed between OviTex 2S-R layers, while Strattice induced a minimal inflammatory response. Strattice retained higher maximum load at 3 (46.3 ± 27.4 N/cm vs 9.5 ± 3.2 N/cm, p = 0.041) and 6 weeks (28.6 ± 14.1 N/cm vs 7.0 ± 3.0 N/cm, p = 0.029). In primates, OviTex 1S-P exhibited loss of composite mesh integrity whereas Strattice integrated into host tissue with minimal inflammation and retained higher maximum load at 1 month than OviTex 1S-P (66.8 ± 43.4 N/cm vs 9.6 ± 4.4 N/cm; p = 0.151). CONCLUSIONS Strattice retained greater mechanical strength as shown by lower susceptibility to collagenase degradation than OviTex 2S-R in vitro, as well as higher maximum load and improved host biologic response than OviTex 2S-R in rodents and OviTex 1S-P in primates.
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Affiliation(s)
- J Lombardi
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - E Stec
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - M Edwards
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - T Connell
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA
| | - M Sandor
- Allergan Aesthetics, an AbbVie Company, 4 Millennium Way, Branchburg, NJ, 08876, USA.
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Kasperska A, Borowczak J, Szczerbowski K, Stec E, Ahmadi N, Szylber Ł. Current challenges in targeting tumor desmoplasia to improve the efficacy of immunotherapy. Curr Cancer Drug Targets 2021; 21:919-931. [PMID: 34525931 DOI: 10.2174/1568009621666210825101456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
Desmoplasia is crucial for the development, progression and treatment of immune-resistant malignancies. and treatment of immune-resistant malignancies. Targeting desmoplasia-related metabolic pathways appears to be an interesting approach to expand our stock of disposable anti-tumor agents.CXCL12/CXCR4 axis inhibition reduces fibrosis, alleviates immunosuppression and significantly enhances the efficacy of PD-1 immunotherapy. CD40L substitute therapy may increase the activity of T-cells, downregulate CD40+, prolong patients' survival and prevent cancer progression. Although FAPα antagonists used in preclinical models did not lead to permanent cure, an alleviation of immune-resistance, modification of desmoplasia and a decrease in angiogenesis were observed. Targeting DDR2 may enhance the effect of anti-PD-1 treatment in multiple neoplasm cell lines and has the ability to overcome the adaptation to BRAF-targeted therapy in melanoma. Reprogramming desmoplasia could potentially cooperate not only with present treatment, but also other potential therapeutic targets. We present the most promising metabolic pathways related to desmoplasia and discuss the emerging strategies to improve the efficacy of immunotherapy.
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Affiliation(s)
- Anna Kasperska
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun. Poland
| | - Jędrzej Borowczak
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun. Poland
| | - Krzysztof Szczerbowski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun. Poland
| | - Ewa Stec
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun. Poland
| | - Navid Ahmadi
- Department of Cardiothoracic Surgery, Royal Papworth Hospital, Cambridge. United Kingdom
| | - Łukasz Szylber
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun. Poland
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Borowczak J, Szczerbowski K, Stec E, Grzanka D, Szylberg Ł. CDK9: Therapeutic Perspective in HCC Therapy. Curr Cancer Drug Targets 2021; 20:318-324. [PMID: 32048975 DOI: 10.2174/1568009620666200212124357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 11/22/2022]
Abstract
CDK9 is an important cell-cycle control enzyme essential in transcription, elongation, and mRNA maturation. Overexpression of CDK9 has been reported in several diseases, including acute lymphoblastic leukemia, chronic lymphocytic leukemia, and malignant melanoma. Recent research revealed that CDK9-inhibitors have a major impact on the induction of apoptosis in hepatocellular carcinoma (HCC) cell lines. Despite surprisingly promising results in in vitro and in vivo research, no CDK9 related therapy is currently allowed in cases of HCC. Furthermore, due to their high specificity, the inhibitors had no effects on unaltered hepatocytes and no toxic effects were shown. Considering that they were well tolerated and showed relatively few severe side-effects in mice, CDK9- inhibitors would seem to be promising targets in HCC biomarker-guided immunotherapy. Studies have verified that CDK9 has a pivotal role in c-Myc-mediated tumor growth and CDK9 inhibitors inhibit not only its progression but diametrically decrease both the mass and size of HCC nodules. CDK9-inhibitors seem to be a promising target in HCC treatment.
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Affiliation(s)
- Jędrzej Borowczak
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Krzysztof Szczerbowski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Ewa Stec
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Dariusz Grzanka
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Łukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Torun, Poland.,Department of Pathomorphology, Military Clinical Hospital, Bydgoszcz, Poland
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Sheng R, Chen Y, Yung Gee H, Stec E, Melowic HR, Blatner NR, Tun MP, Kim Y, Källberg M, Fujiwara TK, Hye Hong J, Pyo Kim K, Lu H, Kusumi A, Goo Lee M, Cho W. Cholesterol modulates cell signaling and protein networking by specifically interacting with PDZ domain-containing scaffold proteins. Nat Commun 2013; 3:1249. [PMID: 23212378 PMCID: PMC3526836 DOI: 10.1038/ncomms2221] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 10/22/2012] [Indexed: 02/06/2023] Open
Abstract
Cholesterol is known to modulate the physical properties of cell membranes but its direct involvement in cellular signaling has not been thoroughly investigated. Here we show that cholesterol specifically binds many PDZ domains found in scaffold proteins, including the N-terminal PDZ domain of NHERF1/EBP50. This modular domain has a cholesterol-binding site topologically distinct from its canonical protein-binding site and serves as a dual specificity domain that bridges the membrane and juxta-membrane signaling complexes. Disruption of the cholesterol binding activity of NHERF1 largely abrogates its dynamic colocalization with and activation of cystic fibrosis transmembrane conductance regulator, one of its binding partners in the plasma membrane of mammalian cells. At least seven more PDZ domains from other scaffold proteins also bind cholesterol and have cholesterol-binding sites, suggesting that cholesterol modulates cell signaling through direct interactions with these scaffold proteins. This mechanism may provide an alternative explanation for the formation of signaling platforms in cholesterol-rich membrane domains.
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Affiliation(s)
- Ren Sheng
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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Stec E, Afsari HS, Kurilova S, Cho W. In situ Quantification of Cellular Cholesterol using a Molecular Sensor. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.lb89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ewa Stec
- ChemistryUniversity of IllinoisChicagoIL
| | | | | | - Wonhwa Cho
- ChemistryUniversity of IllinoisChicagoIL
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Szalewska-Palasz A, Johansson LUM, Bernardo LMD, Skärfstad E, Stec E, Brännström K, Shingler V. Properties of RNA Polymerase Bypass Mutants. J Biol Chem 2007; 282:18046-18056. [PMID: 17456470 DOI: 10.1074/jbc.m610181200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial nutritional and stress alarmone ppGpp and its co-factor DksA directly bind RNA polymerase to regulate its activity at certain sigma70-dependent promoters. A number of promoters that are dependent on alternative sigma-factors function poorly in the absence of ppGpp. These include the Pseudomonas-derived sigma54-dependent Po promoter and several other sigma54-promoters, the transcription from which is essentially abolished in Escherichia coli devoid of ppGpp and DksA. However, ppGpp and DksA have no apparent effect on reconstituted in vitro sigma54-transcription, which suggests an indirect mechanism of control. Here we report analysis of five hyper-suppressor mutants within the beta- and beta'-subunits of core RNA polymerase that allow high levels of transcription from the sigma54-Po promoter in the absence of ppGpp. Using in vitro transcription and competition assays, we present evidence that these core RNA polymerase mutants are defective in one or both of two properties that could combine to explain their hyper-suppressor phenotypes: (i) modulation of competitive association with sigma-factors to favor sigma54-holoenzyme formation over that with sigma70, and (ii) reduced innate stability of RNA polymerase-promoter complexes, which mimics the essential effects of ppGpp and DksA for negative regulation of stringent sigma70-promoters. Both these properties of the mutant holoenzymes support a recently proposed mechanism for regulation of sigma54-transcription that depends on the potent negative effects of ppGpp and DksA on transcription from powerful stringent sigma70-promoters, and suggests that stringent regulation is a key mechanism by which the activity of alternative sigma-factors is controlled to meet cellular requirements.
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Affiliation(s)
- Agnieszka Szalewska-Palasz
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden; Department of Molecular Biology, University of Gdansk, 80822 Gdansk, Poland
| | | | | | - Eleonore Skärfstad
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ewa Stec
- Department of Molecular Biology, University of Gdansk, 80822 Gdansk, Poland
| | | | - Victoria Shingler
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.
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