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Article ; Online: RNA-protein interactomes as invaluable resources to study RNA viruses: Insights from SARS CoV-2 studies.

Koliński, Marcin / Kałużna, Ewelina / Piwecka, Monika

2022 Volume 13, Issue 6, Page(s) e1727

Abstract: Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential for the successful development of therapeutic strategies against the COVID-19 pandemic. Numerous studies have focused on the ... ...

Abstract	Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential for the successful development of therapeutic strategies against the COVID-19 pandemic. Numerous studies have focused on the identification of host factors and cellular pathways involved in the viral replication cycle. The speed and magnitude of hijacking the translation machinery of host mRNA, and shutting down host transcription are still not well understood. Since SARS-CoV-2 relies on host RNA-binding proteins for the infection progression, several efforts have been made to define the SARS-CoV-2 RNA-bound proteomes (RNA-protein interactomes). Methodologies that enable the systemic capture of protein interactors of given RNA in vivo have been adapted for the identification of the SARS-CoV-2 RNA interactome. The obtained proteomic data aided by genome-wide and targeted CRISPR perturbation screens, revealed host factors with either pro- or anti-viral activity and highlighted cellular processes and factors involved in host response. We focus here on the recent studies on SARS-CoV-2 RNA-protein interactomes, with regard to both the technological aspects of RNA interactome capture methods and the obtained results. We also summarize several related studies, which were used in the interpretation of the SARS-CoV-2 RNA-protein interactomes. These studies provided the selection of host factors that are potentially suitable candidates for antiviral therapy. Finally, we underscore the importance of RNA-protein interactome studies in regard to the effective development of antiviral strategies against current and future threats. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells.
MeSH term(s)	Humans ; SARS-CoV-2 ; Pandemics ; COVID-19 ; RNA, Viral/genetics ; Proteomics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-03-27
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1727
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Article: Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation

Koliński, Michał / Kmiecik, Sebastian / Dec, Robert / Piejko, Marcin / Mak, Paweł / Dzwolak, Wojciech

International journal of biological macromolecules. 2020 Apr. 15, v. 149

2020

Abstract: In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain ‘H-fragment’. The H- ... ...

Abstract	In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain ‘H-fragment’. The H-fragment retains several cleavage sites for pepsin. However, under favorable conditions H-monomers rapidly self-assemble into proteolysis-resistant amyloid fibrils whose composition provides snapshots of early and intermediate stages of the proteolysis. In this work, we report a remarkable agreement of experimentally determined and simulation-predicted cleavage sites on different stages of the proteolysis. Prediction of cleavage sites was based on the comprehensive analysis of the docking interactions from direct simulation of coupled folding and binding of insulin (or its cleaved derivatives) to pepsin. The most frequent interactions were found to be between the pepsin's active site, or its direct vicinity, and the experimentally determined insulin cleavage sites, which suggest that the docking interactions govern the proteolytic process.
Keywords	active sites ; amyloid ; insulin ; models ; pepsin ; prediction ; proteolysis
Language	English
Dates of publication	2020-0415
Size	p. 1151-1160.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.01.253
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Article ; Online: Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation.

Koliński, Michał / Kmiecik, Sebastian / Dec, Robert / Piejko, Marcin / Mak, Paweł / Dzwolak, Wojciech

International journal of biological macromolecules

2020 Volume 149, Page(s) 1151–1160

Abstract	In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain 'H-fragment'. The H-fragment retains several cleavage sites for pepsin. However, under favorable conditions H-monomers rapidly self-assemble into proteolysis-resistant amyloid fibrils whose composition provides snapshots of early and intermediate stages of the proteolysis. In this work, we report a remarkable agreement of experimentally determined and simulation-predicted cleavage sites on different stages of the proteolysis. Prediction of cleavage sites was based on the comprehensive analysis of the docking interactions from direct simulation of coupled folding and binding of insulin (or its cleaved derivatives) to pepsin. The most frequent interactions were found to be between the pepsin's active site, or its direct vicinity, and the experimentally determined insulin cleavage sites, which suggest that the docking interactions govern the proteolytic process.
MeSH term(s)	Amino Acid Sequence ; Amyloid/metabolism ; Animals ; Biophysical Phenomena ; Cattle ; Insulin/metabolism ; Kinetics ; Molecular Docking Simulation ; Pepsin A/metabolism ; Peptides/chemistry ; Peptides/metabolism ; Proteolysis ; Swine
Chemical Substances	Amyloid ; Insulin ; Peptides ; Pepsin A (EC 3.4.23.1)
Language	English
Publishing date	2020-01-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.01.253
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Article ; Online: Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP).

Maatz, Henrike / Kolinski, Marcin / Hubner, Norbert / Landthaler, Markus

Current protocols in molecular biology

2017 Volume 118, Page(s) 27.6.1–27.6.19

Abstract: RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA- ... ...

Abstract	RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA-binding sites is essential, and CLIP-seq methods have been developed to elucidate protein/RNA interactions at high resolution. CLIP-seq combines protein/RNA UV-crosslinking with immunoprecipitation (CLIP) followed by high-throughput sequencing of crosslinked RNA fragments. To overcome the limitations of low RNA-protein crosslinking efficiency in standard CLIP-seq, photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) has been developed. Here, living cells or whole organisms are fed photo-activatable nucleoside analogs that are incorporated into nascent RNA transcripts before UV treatment. This allows greater crosslinking efficiency at comparable radiation doses for enhanced RNA recovery and separation of crosslinked target RNA fragments from background RNA degradation products. Moreover, it facilitates the generation of specific UV-induced mutations that mark the crosslinking nucleotide and allow transcriptome-wide identification of RBP binding sites at single-nucleotide resolution. © by 2017 John Wiley & Sons, Inc.
MeSH term(s)	Animals ; Base Sequence ; Binding Sites ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunoprecipitation/methods ; Photochemical Processes ; Protein Binding ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA-Binding Proteins/metabolism ; Ribonucleosides/chemistry ; Ribonucleosides/genetics ; Ribonucleosides/metabolism ; Transcriptome
Chemical Substances	RNA-Binding Proteins ; Ribonucleosides ; RNA (63231-63-0)
Language	English
Publishing date	2017-04-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1934-3647
ISSN (online)	1934-3647
DOI	10.1002/cpmb.35
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Article ; Online: Taxonomic position and phylogeny of the genus Vargasiella (Orchidaceae, Vandoideae) based on molecular and morphological evidence.

Szlachetko, Dariusz L / Górniak, Marcin / Kolanowska, Marta / Mytnik-Ejsmont, Joanna / Kowalkowska, Agnieszka K / Rutkowski, Piotr / Koliński, Tomasz

PloS one

2014 Volume 9, Issue 6, Page(s) e98472

Abstract: Since the description of the Neotropical genus Vargasiella in 1952, its taxonomic position has remained unclear, mainly due to a lack of sufficient data. In this study, the taxonomic position of Vargasiella was revised based on the outcomes of macro- and ...

Abstract	Since the description of the Neotropical genus Vargasiella in 1952, its taxonomic position has remained unclear, mainly due to a lack of sufficient data. In this study, the taxonomic position of Vargasiella was revised based on the outcomes of macro- and micromorphological studies, analyses of selected molecular markers and ecological methods of niche distribution modeling. The phylogenetic relationships were inferred using three DNA markers: matK, trnL-F and ITS sequences. The morphological studies included the analysis of macromorphological features of herbarium specimens as well as micromorphological examination of preserved flowers. The ecological niche modeling was applied to identify the distribution of the suitable niches of the studied taxa. The relationships between Vargasiella and most similar taxa remain unresolved based on the molecular analysis. The outcomes from the morphological studies indicated significant differences between Vargasiella, Warrea and Warreopsis. Moreover, a niche shift in response to changing climate after the last glacial maximum is observed in Vargasiella, while no substantial changes in the occupied habitats were identified in the other related taxa. The clocktree of the Zygopetaleae estimated from the matK gene indicated that the most recent common ancestors of Vargasiella, Warrea and Warreopsis originated in the Miocene, while the divergence time for Vargasiella and Warrea was assessed at approximately 5.4 Ma ago. Vargasiella seems to be an outshoot of the main branch of evolution of the Zygopetaleae. It is noteworthy that the Vargasiella-Warrea dichotomy could have taken place later than the divergence of Warreopsis from the mutual lineage. The molecular analysis and morphological data suggest that Vargasiella and Warrea could have evolved from a common ancestor. Accumulation of morphological differences and acceleration of the evolution of Vargasiella were more intensive than in other Warreinae and this could probably be synchronized with adaptation to different climatic conditions.
MeSH term(s)	DNA, Plant/genetics ; Orchidaceae/classification ; Orchidaceae/metabolism ; Phylogeny
Chemical Substances	DNA, Plant
Language	English
Publishing date	2014-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0098472
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Article ; Online: The mRNA-bound proteome of the early fly embryo.

Wessels, Hans-Hermann / Imami, Koshi / Baltz, Alexander G / Kolinski, Marcin / Beldovskaya, Anastasia / Selbach, Matthias / Small, Stephen / Ohler, Uwe / Landthaler, Markus

Genome research

2016 Volume 26, Issue 7, Page(s) 1000–1009

Abstract: Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins ( ... ...

Abstract	Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRNA interactome capture methods to identify RBPs bound to polyadenylated transcripts within the first 2 h of Drosophila melanogaster embryogenesis. We identified a high-confidence set of 476 putative RBPs and confirmed RNA-binding activities for most of 24 tested candidates. Most proteins in the interactome are known RBPs or harbor canonical RBP features, but 99 exhibited previously uncharacterized RNA-binding activity. mRNA-bound RBPs and TFs exhibit distinct expression dynamics, in which the newly identified RBPs dominate the first 2 h of embryonic development. Integrating our resource with in situ hybridization data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation.
MeSH term(s)	Animals ; Drosophila Proteins/metabolism ; Drosophila melanogaster/embryology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Embryonic Development ; Female ; Gene Expression Regulation, Developmental ; Male ; Protein Binding ; Proteome/metabolism ; RNA, Messenger/metabolism ; RNA-Binding Proteins/metabolism
Chemical Substances	Drosophila Proteins ; Proteome ; RNA, Messenger ; RNA-Binding Proteins
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.200386.115
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Article ; Online: Taxonomic position and phylogeny of the genus Vargasiella (Orchidaceae, Vandoideae) based on molecular and morphological evidence.

Dariusz L Szlachetko / Marcin Górniak / Marta Kolanowska / Joanna Mytnik-Ejsmont / Agnieszka K Kowalkowska / Piotr Rutkowski / Tomasz Koliński

PLoS ONE, Vol 9, Iss 6, p e

2014 Volume 98472

Abstract	Since the description of the Neotropical genus Vargasiella in 1952, its taxonomic position has remained unclear, mainly due to a lack of sufficient data. In this study, the taxonomic position of Vargasiella was revised based on the outcomes of macro- and micromorphological studies, analyses of selected molecular markers and ecological methods of niche distribution modeling. The phylogenetic relationships were inferred using three DNA markers: matK, trnL-F and ITS sequences. The morphological studies included the analysis of macromorphological features of herbarium specimens as well as micromorphological examination of preserved flowers. The ecological niche modeling was applied to identify the distribution of the suitable niches of the studied taxa. The relationships between Vargasiella and most similar taxa remain unresolved based on the molecular analysis. The outcomes from the morphological studies indicated significant differences between Vargasiella, Warrea and Warreopsis. Moreover, a niche shift in response to changing climate after the last glacial maximum is observed in Vargasiella, while no substantial changes in the occupied habitats were identified in the other related taxa. The clocktree of the Zygopetaleae estimated from the matK gene indicated that the most recent common ancestors of Vargasiella, Warrea and Warreopsis originated in the Miocene, while the divergence time for Vargasiella and Warrea was assessed at approximately 5.4 Ma ago. Vargasiella seems to be an outshoot of the main branch of evolution of the Zygopetaleae. It is noteworthy that the Vargasiella-Warrea dichotomy could have taken place later than the divergence of Warreopsis from the mutual lineage. The molecular analysis and morphological data suggest that Vargasiella and Warrea could have evolved from a common ancestor. Accumulation of morphological differences and acceleration of the evolution of Vargasiella were more intensive than in other Warreinae and this could probably be synchronized with adaptation to different climatic ...
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article: Protein modeling with reduced representation: statistical potentials and protein folding mechanism.

Ekonomiuk, Dariusz / Kielbasinski, Marcin / Kolinski, Andrzej

Acta biochimica Polonica

2005 Volume 52, Issue 4, Page(s) 741–748

Abstract: A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics ... ...

Abstract	A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon beta-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the beta-sheet.
MeSH term(s)	Biophysical Phenomena ; Biophysics ; Computer Simulation ; Models, Molecular ; Monte Carlo Method ; Protein Conformation ; Protein Folding ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2005
Publishing country	Poland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	595762-x
ISSN	1734-154X ; 0001-527X
ISSN (online)	1734-154X
ISSN	0001-527X
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Article: Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.

Hoffmann, Marcin / Eitner, Krystian / von Grotthuss, Marcin / Rychlewski, Leszek / Banachowicz, Ewa / Grabarkiewicz, Tomasz / Szkoda, Tomasz / Kolinski, Andrzej

Journal of computer-aided molecular design

2006 Volume 20, Issue 5, Page(s) 305–319

Abstract: The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, ... ...

Abstract	The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.
MeSH term(s)	Amino Acid Sequence ; Catalytic Domain ; Conserved Sequence ; DNA Helicases/antagonists & inhibitors ; DNA Helicases/chemistry ; Drug Design ; Enzyme Inhibitors/pharmacology ; Models, Molecular ; Molecular Sequence Data ; SARS Virus/enzymology ; Sequence Alignment ; Structural Homology, Protein ; Thermodynamics
Chemical Substances	Enzyme Inhibitors ; DNA Helicases (EC 3.6.4.-)
Keywords	covid19
Language	English
Publishing date	2006-09-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-006-9057-z
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Article ; Online: Using an on-site laboratory for fecal steroid analysis in wild white-faced capuchins.

General and comparative endocrinology

2022 Volume 329, Page(s) 114109

Abstract: Hormone laboratories located "on-site" where field studies are being conducted have a number of advantages. On-site laboratories allow hormone analyses to proceed in near-real-time, minimize logistics of sample permits/shipping, contribute to in-country ... ...

Abstract	Hormone laboratories located "on-site" where field studies are being conducted have a number of advantages. On-site laboratories allow hormone analyses to proceed in near-real-time, minimize logistics of sample permits/shipping, contribute to in-country capacity-building, and (our focus here) facilitate cross-site collaboration through shared methods and a shared laboratory. Here we provide proof-of-concept that an on-site hormone laboratory (the Taboga Field Laboratory, located in the Taboga Forest Reserve, Costa Rica) can successfully run endocrine analyses in a remote location. Using fecal samples from wild white-faced capuchins (Cebus imitator) from three Costa Rican forests, we validate the extraction and analysis of four steroid hormones (glucocorticoids, testosterone, estradiol, progesterone) across six assays (DetectX® and ISWE, all from Arbor Assays). Additionally, as the first collaboration across three long-term, wild capuchin field sites (Lomas Barbudal, Santa Rosa, Taboga) involving local Costa Rican collaborators, this laboratory can serve as a future hub for collaborative exchange.
MeSH term(s)	Animals ; Cebus capucinus ; Laboratories ; Cebus ; Feces ; Testosterone ; Costa Rica
Chemical Substances	Testosterone (3XMK78S47O)
Language	English
Publishing date	2022-08-22
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	1851-x
ISSN	1095-6840 ; 0016-6480
ISSN (online)	1095-6840
ISSN	0016-6480
DOI	10.1016/j.ygcen.2022.114109
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