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Article ; Online: Tacrolimus Metabolite M-III May Have Nephrotoxic and Myelotoxic Effects and Increase the Incidence of Infections in Kidney Transplant Recipients.

Zegarska, J / Hryniewiecka, E / Zochowska, D / Samborowska, E / Jazwiec, R / Borowiec, A / Tszyrsznic, W / Chmura, A / Nazarewski, S / Dadlez, M / Paczek, L

Transplantation proceedings

2016 Volume 48, Issue 5, Page(s) 1539–1542

Abstract: ... of this study was quantification of the 2 major Tac metabolites, 13-O-demethyl (M-I) and 15-O-demethyl (M-III ... M-I, and M-III were measured with the use of liquid chromatography combined ... with tandem mass spectrometry (LC-MS-MS).: Results: There was a negative correlation between M-III levels and estimated ...

Abstract	Background: Tacrolimus (Tac) is one of the most commonly used immunosuppressive drugs after solid organ transplantation. Eight Tac metabolites have been described, but their clinical importance remains unclear. The aim of this study was quantification of the 2 major Tac metabolites, 13-O-demethyl (M-I) and 15-O-demethyl (M-III), in kidney transplant recipients and to link them with parameters of kidney and liver function, peripheral blood cell counts, and infection incidence. Methods: In 81 kidney transplant recipients, concentrations of Tac, M-I, and M-III were measured with the use of liquid chromatography combined with tandem mass spectrometry (LC-MS-MS). Results: There was a negative correlation between M-III levels and estimated glomerular filtration rate (eGFR; r = -0.244; P < .05). Also, a negative correlation between M-III concentrations and red blood cell count (RBC) was found (r = -0.349; P < .05). Neither concentrations of Tac nor of M-I correlated with eGFR or RBC. M-I, M-III, and Tac were not related to alanine aminotransferase activity. Significantly higher Tac and M-III concentrations in the group with all types of infections in comparison with the group without infections were observed (6.95 ± 2.09 ng/mL vs 5.73 ± 2.43 ng/mL [P = .03] and 0.27 ± 0.17 ng/mL vs 0.20 ± 0.11 ng/mL [P = .04], respectively). Conclusions: The results suggest that higher concentrations of M-III may have a nephrotoxic or myelotoxic effect and result in higher incidence of infections. Further studies are needed to confirm if monitoring of M-III could minimalize adverse effects such as nephrotoxicity or infections.
MeSH term(s)	Adult ; Chromatography, Liquid ; Dydrogesterone/adverse effects ; Dydrogesterone/analogs & derivatives ; Dydrogesterone/blood ; Female ; Humans ; Immunosuppressive Agents/adverse effects ; Immunosuppressive Agents/metabolism ; Incidence ; Infection/epidemiology ; Kidney/drug effects ; Kidney Transplantation ; Male ; Middle Aged ; Tacrolimus/adverse effects ; Tacrolimus/metabolism ; Tandem Mass Spectrometry ; Transplant Recipients
Chemical Substances	Immunosuppressive Agents ; 21-hydroxy-9beta,10alpha-pregna-5,7-diene-3-ol-20-one (86416-32-2) ; Dydrogesterone (90I02KLE8K) ; Tacrolimus (WM0HAQ4WNM)
Language	English
Publishing date	2016-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	82046-5
ISSN	1873-2623 ; 0041-1345
ISSN (online)	1873-2623
ISSN	0041-1345
DOI	10.1016/j.transproceed.2015.12.133
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Article: A micro-flow, high-pH, reversed-phase peptide fractionation and collection system for targeted and in-depth proteomics of low-abundance proteins in limiting samples.

Zurawska, Marta / Basik, Mark / Aguilar-Mahecha, Adriana / Dadlez, Michal / Domanski, Dominik

MethodsX

2023 Volume 11, Page(s) 102306

Abstract: We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30-60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and ... ...

Abstract	We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30-60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and robustness. The method is applicable to targeted mass spectrometry approaches and to in-depth proteomic studies where the amount of sample is limited. Using targeted proteomics with peptide standards, we present the method's analytical parameters, and potential in increasing the detection of low-abundance proteins that are difficult to quantify with direct targeted or global LC-MS analyses. This fractionation system increased peptide signals by up to 18-fold, while maintaining high quantitative precision, with high fractionation reproducibility across varied sample sets. In real applications, it increased the detection of targeted endogenous peptides by two-fold in a 25 cell-cycle-control protein panel, and in-depth MS analyses of nuclear extracts, it allowed the detection of up to 8,896 proteins with 138,417 peptides in 24-concatenated fractions compared to 3,344 proteins with 23,093 peptides without fractionation. In a relevant biological problem of CDK4/6-inhibitors and breast cancer, the method reproduced known information and revealed novel insights, highlighting that it can be successfully applied in studies involving low-abundance proteins and limited samples. •Tested nine high-pH buffer/solvent systems to obtain a robust, effective, and reproducible micro-flow fractionation method which was devoid of commonly encountered LC clogging/pressure issues after months of use.•Peptide enrichment method to improve detection and quantitation of low-abundance proteins in targeted and in-depth proteomic studies.•Can be applied to diverse protein samples where the available amount is limited.
Language	English
Publishing date	2023-07-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2830212-6
ISSN	2215-0161
ISSN	2215-0161
DOI	10.1016/j.mex.2023.102306
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Article ; Online: Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach.

Negrutskii, Boris S / Porubleva, Larysa V / Malinowska, Agata / Novosylna, Oleksandra V / Dadlez, Michal / Knudsen, Charlotte R

Advances in protein chemistry and structural biology

2023 Volume 138, Page(s) 67–99

Abstract: Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in ... ...

Abstract	Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.
MeSH term(s)	Animals ; Humans ; Mammals ; Protein Biosynthesis ; Protein Isoforms/genetics ; Proteomics
Chemical Substances	Protein Isoforms ; EEF1A1 protein, human ; EEF1A2 protein, human
Language	English
Publishing date	2023-12-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2473077-4
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2023.10.001
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Article ; Online: Alternative approach to pediatric cardiac quality assessment for low-volume centers.

Delaney, Amy E / Dadlez, Nina M / Marshall, Audrey C

Congenital heart disease

2019 Volume 14, Issue 4, Page(s) 665–670

Abstract: Background: In pediatric cardiac care, many centers participate in multiple, national, domain-specific registries, as a major component of their quality assessment and improvement efforts. Small cardiac programs, whose clinical activities and scale may ... ...

Abstract	Background: In pediatric cardiac care, many centers participate in multiple, national, domain-specific registries, as a major component of their quality assessment and improvement efforts. Small cardiac programs, whose clinical activities and scale may not be well-suited to this approach, need alternative methods to assess and track quality. Methods: We conceived of and piloted a rapid-approach cardiac quality assessment, intended to encompass multiple aspects of the service line, in a low-volume program. The assessment incorporated previously identified measures, drawn from multiple sources, and ultimately relied on retrospective chart review. Results: A collaborative, multidisciplinary team formed and came to consensus on quality metrics pertaining to 3 chosen areas of clinical activity in the program. Despite the use of multiple different data sources and the need for manual chart review in data collection, a rich assessment of these program components was completed for presentation in 6 weeks. Conclusions: While small programs may not participate in the spectrum of cardiac care registries available, these same centers can benefit from them by adapting some of their validated metrics for use in internal, self-maintained quality reports. Our pilot of this alternative approach revealed opportunities for improved quality assessment practices; the product can serve as a baseline for future prospective assessment and reporting, as well as longitudinal internal benchmarking.
MeSH term(s)	Benchmarking/standards ; Cardiology/standards ; Child ; Heart Defects, Congenital/therapy ; Hospitals, Low-Volume/standards ; Humans ; Program Evaluation ; Quality Indicators, Health Care ; Registries ; Retrospective Studies ; United States
Language	English
Publishing date	2019-07-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2274321-2
ISSN	1747-0803 ; 1747-079X
ISSN (online)	1747-0803
ISSN	1747-079X
DOI	10.1111/chd.12821
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Article ; Online: Interaction interface in the C-terminal parts of centriole proteins Sas6 and Ana2.

Fatalska, Agnieszka / Dzhindzhev, Nikola S / Dadlez, Michal / Glover, David M

Open biology

2020 Volume 10, Issue 11, Page(s) 200221

Abstract: The centriole is a ninefold symmetrical structure found at the core of centrosomes and, as a basal body, at the base of cilia, whose conserved duplication is regulated by Plk4 kinase. Plk4 phosphorylates a single serine residue at the N-terminus of Ana2 ... ...

Abstract	The centriole is a ninefold symmetrical structure found at the core of centrosomes and, as a basal body, at the base of cilia, whose conserved duplication is regulated by Plk4 kinase. Plk4 phosphorylates a single serine residue at the N-terminus of Ana2 to promote Ana2's loading to the site of procentriole formation. Four conserved serines in Ana2's STAN motif are then phosphorylated by Plk4, enabling Sas6 recruitment. Crystallographic data indicate that the coiled-coil domain of Ana2 forms a tetramer but the structure of full-length Ana2 has not been solved. Here, we have employed hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) to uncover the conformational dynamics of Ana2, revealing the high flexibility of this protein with one rigid region. To determine the elusive nature of the interaction surfaces between Ana2 and Sas6, we have confirmed complex formation between the phosphomimetic form of Ana2 (Ana2-4D) and Sas6
MeSH term(s)	Amino Acid Sequence ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Drosophila Proteins/chemistry ; Drosophila Proteins/metabolism ; Mass Spectrometry ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Interaction Maps
Chemical Substances	Ana2 protein, Drosophila ; Cell Cycle Proteins ; Drosophila Proteins ; Sas-6 protein, Drosophila
Language	English
Publishing date	2020-11-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.200221
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Article ; Online: Insight into the Structural Dynamics of the Lysenin During Prepore-to-Pore Transition Using Hydrogen-Deuterium Exchange Mass Spectrometry.

Kulma, Magdalena / Dadlez, Michał / Kwiatkowska, Katarzyna

Toxins

2019 Volume 11, Issue 8

Abstract: Lysenin is a pore-forming toxin of the aerolysin family, which is derived from coelomic fluid of the ... ...

Abstract	Lysenin is a pore-forming toxin of the aerolysin family, which is derived from coelomic fluid of the earthworm
MeSH term(s)	Crystallography, X-Ray ; Hydrogen Deuterium Exchange-Mass Spectrometry/methods ; Mutation ; Protein Conformation ; Thermodynamics ; Toxins, Biological/chemistry ; Toxins, Biological/genetics
Chemical Substances	Toxins, Biological ; lysenin
Language	English
Publishing date	2019-08-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518395-3
ISSN	2072-6651 ; 2072-6651
ISSN (online)	2072-6651
ISSN	2072-6651
DOI	10.3390/toxins11080462
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Article ; Online: Author Correction: A heterotypic assembly mechanism regulates CHIP E3 ligase activity.

Das, Aniruddha / Thapa, Pankaj / Santiago, Ulises / Shanmugam, Nilesh / Banasiak, Katarzyna / Dązbrowska, Katarzyna / Nolte, Hendrik / Szulc, Natalia A / Gathungu, Rose M / Cysewski, Dominik / Krüeger, Marcus / Dadlez, Michał / Nowotny, Marcin / Camacho, Carlos J / Hoppe, Thorsten / Pokrzywa, Wojciech

The EMBO journal

2024 Volume 43, Issue 6, Page(s) 1110–1111

Language	English
Publishing date	2024-02-22
Publishing country	England
Document type	Published Erratum
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.1038/s44318-024-00042-3
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Article ; Online: Dissecting SUMO Dynamics by Mass Spectrometry.

Drabikowski, Krzysztof / Dadlez, Michał

Methods in molecular biology (Clifton, N.J.)

2016 Volume 1449, Page(s) 291–298

Abstract: Protein modification by SUMO proteins is one of the key posttranslational modifications in eukaryotes. Here, we describe a workflow to analyze SUMO dynamics in response to different stimuli, purify SUMO conjugates, and analyze the changes in SUMOylation ... ...

Abstract	Protein modification by SUMO proteins is one of the key posttranslational modifications in eukaryotes. Here, we describe a workflow to analyze SUMO dynamics in response to different stimuli, purify SUMO conjugates, and analyze the changes in SUMOylation level in organisms, tissues, or cell culture. We present a protocol for lysis in denaturing conditions that is compatible with downstream IMAC and antibody affinity purification, followed by mass spectrometry and data analysis.
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-3756-1_18
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Article ; Online: A model of full-length RAGE in complex with S100B.

Moysa, Alexander / Steczkiewicz, Kamil / Niedzialek, Dorota / Hammerschmid, Dietmar / Zhukova, Lilia / Sobott, Frank / Dadlez, Michal

Structure (London, England : 1993)

2021 Volume 29, Issue 9, Page(s) 989–1002.e6

Abstract: The receptor for advanced glycation end products (RAGE) is an immunoglobulin-type multiligand transmembrane protein expressed in numerous cell types, including the central nervous system cells. RAGE interaction with S100B, released during brain tissue ... ...

Abstract	The receptor for advanced glycation end products (RAGE) is an immunoglobulin-type multiligand transmembrane protein expressed in numerous cell types, including the central nervous system cells. RAGE interaction with S100B, released during brain tissue damage, leads to RAGE upregulation and initialization of a spiral proinflammatory associated with different neural disorders. Here, we present the structural characterization of the hetero-oligomeric complex of the full-length RAGE with S100B, obtained by a combination of mass spectrometry-based methods and molecular modeling. We predict that RAGE functions as a tightly packed tetramer exposing a positively charged surface formed by V domains for S100B binding. Based on HDX results we demonstrate an allosteric coupling of the distal extracellular V domains and the transmembrane region, indicating a possible mechanism of signal transmission by RAGE across the membrane. Our model provides an insight into RAGE-ligand interactions, providing a basis for the rational design of the therapeutic modifiers of its activity.
MeSH term(s)	Animals ; Binding Sites ; Humans ; Molecular Docking Simulation ; Protein Binding ; Receptor for Advanced Glycation End Products/chemistry ; Receptor for Advanced Glycation End Products/metabolism ; S100 Calcium Binding Protein beta Subunit/chemistry ; S100 Calcium Binding Protein beta Subunit/metabolism ; Signal Transduction
Chemical Substances	Receptor for Advanced Glycation End Products ; S100 Calcium Binding Protein beta Subunit
Language	English
Publishing date	2021-04-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.04.002
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Article ; Online: A micro-flow, high-pH, reversed-phase peptide fractionation and collection system for targeted and in-depth proteomics of low-abundance proteins in limiting samples

Zurawska, Marta / Basik, Mark / Aguilar-Mahecha, Adriana / Dadlez, Michal / Domanski, Dominik

MethodsX. 2023 Dec., v. 11 p.102306-

2023

Abstract: We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30–60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and ... ...

Abstract	We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30–60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and robustness. The method is applicable to targeted mass spectrometry approaches and to in-depth proteomic studies where the amount of sample is limited. Using targeted proteomics with peptide standards, we present the method's analytical parameters, and potential in increasing the detection of low-abundance proteins that are difficult to quantify with direct targeted or global LC-MS analyses. This fractionation system increased peptide signals by up to 18-fold, while maintaining high quantitative precision, with high fractionation reproducibility across varied sample sets. In real applications, it increased the detection of targeted endogenous peptides by two-fold in a 25 cell-cycle-control protein panel, and in-depth MS analyses of nuclear extracts, it allowed the detection of up to 8,896 proteins with 138,417 peptides in 24-concatenated fractions compared to 3,344 proteins with 23,093 peptides without fractionation. In a relevant biological problem of CDK4/6-inhibitors and breast cancer, the method reproduced known information and revealed novel insights, highlighting that it can be successfully applied in studies involving low-abundance proteins and limited samples. •Tested nine high-pH buffer/solvent systems to obtain a robust, effective, and reproducible micro-flow fractionation method which was devoid of commonly encountered LC clogging/pressure issues after months of use.•Peptide enrichment method to improve detection and quantitation of low-abundance proteins in targeted and in-depth proteomic studies.•Can be applied to diverse protein samples where the available amount is limited.
Keywords	ammonium bicarbonate ; breast neoplasms ; fractionation ; mass spectrometry ; peptides ; proteomics ; solvents ; Two-dimensional peptide separation ; Peptide fractionation ; High-pH reversed phase liquid chromatography ; Multiple reaction monitoring (MRM) ; Parallel reaction monitoring (PRM) ; Targeted proteomics ; Global proteomics ; Cell-cycle ; CDK4/6 inhibitors ; Micro-flow high-pH reversed-phase LC system for peptide fractionation and collection
Language	English
Dates of publication	2023-12
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	2830212-6
ISSN	2215-0161
ISSN	2215-0161
DOI	10.1016/j.mex.2023.102306
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