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Chyży P, Kulik M, Shinobu A, Re S, Sugita Y, Trylska J. Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proc Natl Acad Sci U S A 2024; 121:e2317197121. [PMID: 38579011 PMCID: PMC11009640 DOI: 10.1073/pnas.2317197121] [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: 10/08/2023] [Accepted: 02/15/2024] [Indexed: 04/07/2024] Open
Abstract
Riboswitches are messenger RNA (mRNA) fragments binding specific small molecules to regulate gene expression. A synthetic N1 riboswitch, inserted into yeast mRNA controls the translation of a reporter gene in response to neomycin. However, its regulatory activity is sensitive to single-point RNA mutations, even those distant from the neomycin binding site. While the association paths of neomycin to N1 and its variants remain unknown, recent fluorescence kinetic experiments indicate a two-step process driven by conformational selection. This raises the question of which step is affected by mutations. To address this, we performed all-atom two-dimensional replica-exchange molecular dynamics simulations for N1 and U14C, U14C[Formula: see text], U15A, and A17G mutants, ensuring extensive conformational sampling of both RNA and neomycin. The obtained neomycin association and binding paths, along with multidimensional free-energy profiles, revealed a two-step binding mechanism, consisting of conformational selection and induced fit. Neomycin binds to a preformed N1 conformation upon identifying a stable upper stem and U-turn motif in the riboswitch hairpin. However, the positioning of neomycin in the binding site occurs at different RNA-neomycin distances for each mutant, which may explain their different regulatory activities. The subsequent induced fit arises from the interactions of the neomycin's N3 amino group with RNA, causing the G9 backbone to rearrange. In the A17G mutant, the critical C6-A17/G17 stacking forms at a closer RNA-neomycin distance compared to N1. These findings together with estimated binding free energies coincide with experiments and elucidate why the A17G mutation decreases and U15A enhances N1 activity in response to neomycin.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
| | - Marta Kulik
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093Warsaw, Poland
| | - Ai Shinobu
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 567-0085Ibaraki, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 351-0198Wako, Japan
- RIKEN Center for Computational Science, 650-0047Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
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2
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Budniak U, Karolak NK, Kulik M, Młynarczyk K, Górna MW, Dominiak PM. The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method. J Phys Chem B 2022; 126:9152-9167. [PMID: 36326196 PMCID: PMC9677429 DOI: 10.1021/acs.jpcb.2c04519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electrostatic energy has a significant contribution to intermolecular interaction energy, especially in biological systems. Unfortunately, precise quantum mechanics calculations are not feasible for large biological systems; hence, simpler calculation methods are required. We propose a method called UBDB+EPMM (University at Buffalo Pseudoatom DataBank + Exact Potential Multipole Moments), which shortens computational time without losing accuracy. Here, we characterize electrostatic interactions in selected complexes of IFIT proteins with RNA. IFIT proteins are effectors of the innate immune system, and by binding foreign RNA, they prevent the synthesis of viral proteins in human host cells; hence, they block the propagation of viruses. We show that by using the UBDB+EPMM method it is possible to describe protein-RNA interactions not only qualitatively but also quantitatively. Looking at the charge penetration contribution to electrostatic interactions, we find all amino acid residues with strong local interactions. Moreover, we confirm that electrostatic interaction of IFIT5 with pppRNA does not depend on the sequence of the RNA.
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Affiliation(s)
- Urszula
Anna Budniak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Natalia Katarzyna Karolak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,Nencki
Institute of Experimental Biology, Polish
Academy of Sciences, ul. Ludwika Pasteura 3, 02-093 Warszawa, Poland
| | - Marta Kulik
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Młynarczyk
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Maria Wiktoria Górna
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,E-mail:
| | - Paulina Maria Dominiak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,E-mail:
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3
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Rybicka P, Kulik M, Chodkiewicz M, Dominiak P. MATTS2021 data bank: application of cluster analysis to interpret electron density of atom types. Acta Cryst Sect A 2022. [DOI: 10.1107/s205327332209475x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Rybicka PM, Kulik M, Chodkiewicz ML, Dominiak PM. Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis. J Chem Inf Model 2022; 62:3766-3783. [PMID: 35943739 PMCID: PMC9400106 DOI: 10.1021/acs.jcim.2c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/29/2022]
Abstract
![]()
The multipole model (MM) uses an aspherical approach
to describe
electron density and can be used to interpret data from X-ray diffraction
in a more accurate manner than using the spherical approximation.
The MATTS (multipolar atom types from theory and statistical clustering)
data bank gathers MM parameters specific for atom types in proteins,
nucleic acids, and organic molecules. However, it was not fully understood
how the electron density of particular atoms responds to their surroundings
and which factors describe the electron density in molecules within
the MM. In this work, by applying clustering using descriptors available
in the MATTS data bank, that is, topology and multipole parameters,
we found the topology features with the biggest impact on the multipole
parameters: the element of the central atom, the number of first neighbors,
and planarity of the group. The similarities in the spatial distribution
of electron density between and within atom type classes revealed
distinct and unique atom types. The quality of existing types can
be improved by adding better parametrization, definitions, and local
coordinate systems. Future development of the MATTS data bank should
lead to a wider range of atom types necessary to construct the electron
density of any molecule.
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Affiliation(s)
- Paulina Maria Rybicka
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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5
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Kulik M, Chodkiewicz ML, Dominiak PM. Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank. Acta Crystallogr D Struct Biol 2022; 78:1010-1020. [PMID: 35916225 PMCID: PMC9344478 DOI: 10.1107/s2059798322005836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/31/2022] [Indexed: 11/10/2022] Open
Abstract
The availability of atomic resolution experimental maps of electrostatic potential from 3D electron diffraction (3D ED) extends the possibility of investigating the electrostatic potential beyond the determination of non-H-atom positions. However, accurate tools to calculate this potential for macromolecules, without the use of expensive quantum calculations, are lacking. The University at Buffalo Data Bank (UBDB) gathers atom types that can be used to calculate accurate electrostatic potential maps via structure-factor calculations. Here, the transferable aspherical atom model (TAAM) is applied with UBDB to investigate theoretically obtained electrostatic potential maps of lysozyme and proteinase K, and compare them with experimental maps from 3D ED. UBDB better reproduces the molecular electrostatic potential of molecules within their entire volume compared with the neutral spherical models used in the popular independent atom model (IAM). Additionally, the theoretical electron-density maps of the studied proteins are shown and compared with the electrostatic potential maps. The atomic displacement parameters (B factors) may affect the electrostatic potential maps in a different way than in the case of electron-density maps. The computational method presented in this study could potentially facilitate the interpretation of the less resolved regions of cryo-electron microscopy density maps and pave the way for distinguishing between different ions/water molecules in the active sites of macromolecules in high-resolution structures, which is of interest for drug-design purposes.
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Affiliation(s)
- Marta Kulik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
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6
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Kulik M, Chodkiewicz ML, Dominiak PM. Theoretical electrostatic potential maps of macromolecules calculated with multipolar electron scattering factors. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321092977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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7
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Dominiak PM, Chodkiewicz ML, Gruza B, Jha KK, Kulik M, Rybicka P, Sypko A. Moving quantum crystallography from sub-atomic XRD to near-atomic 3D-ED. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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8
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Nishima W, Kulik M. Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism. Viruses 2021; 13:v13061126. [PMID: 34208191 PMCID: PMC8230804 DOI: 10.3390/v13061126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
The SARS-CoV-2 virus has now become one of the greatest causes of infectious death and morbidity since the 1918 flu pandemic. Substantial and unprecedented progress has been made in the elucidation of the viral infection process in a short time; however, our understanding of the structure–function dynamics of the spike protein during the membrane fusion process and viral uptake remains incomplete. Employing computational approaches, we use full-length structural models of the SARS-CoV-2 spike protein integrating Cryo-EM images and biophysical properties, which fill the gaps in our understanding. We propose a membrane fusion model incorporating structural transitions associated with the proteolytic processing of the spike protein, which initiates and regulates a series of events to facilitate membrane fusion and viral genome uptake. The membrane fusion mechanism highlights the notable role of the S1 subunit and eventual mature spike protein uptake through the host membrane. Our comprehensive view accounts for distinct neutralizing antibody binding effects targeting the spike protein and the enhanced infectivity of the SARS-CoV-2 variant.
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Affiliation(s)
- Wataru Nishima
- New Mexico Consortium, Los Alamos, NM 87545, USA
- University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-839 Warsaw, Poland;
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Kulik M, Mori T, Sugita Y. Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution. Front Mol Biosci 2021; 8:631854. [PMID: 33842541 PMCID: PMC8025875 DOI: 10.3389/fmolb.2021.631854] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Structure determination using cryo-electron microscopy (cryo-EM) medium-resolution density maps is often facilitated by flexible fitting. Avoiding overfitting, adjusting force constants driving the structure to the density map, and emulating complex conformational transitions are major concerns in the fitting. To address them, we develop a new method based on a three-step multi-scale protocol. First, flexible fitting molecular dynamics (MD) simulations with coarse-grained structure-based force field and replica-exchange scheme between different force constants replicas are performed. Second, fitted Cα atom positions guide the all-atom structure in targeted MD. Finally, the all-atom flexible fitting refinement in implicit solvent adjusts the positions of the side chains in the density map. Final models obtained via the multi-scale protocol are significantly better resolved and more reliable in comparison with long all-atom flexible fitting simulations. The protocol is useful for multi-domain systems with intricate structural transitions as it preserves the secondary structure of single domains.
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Affiliation(s)
- Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan.,RIKEN Center for Computational Science, Kobe, Japan.,RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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10
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Chyży P, Kulik M, Re S, Sugita Y, Trylska J. Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection. Front Mol Biosci 2021; 8:633130. [PMID: 33708793 PMCID: PMC7942488 DOI: 10.3389/fmolb.2021.633130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. One switch, called riboswitch N1, is regulated by aminoglycosides such as neomycin. Nucleobase mutations in the apical loop, although distant from the binding pocket, significantly affect neomycin affinity and riboswitch regulatory efficiency. To explain this influence, we conducted molecular dynamics simulations using generalized replica exchange with solute tempering (gREST). Translation assay of a reporter protein in a yeast system shows that mutating A17 to G in the riboswitch apical loop reduces 6-fold the translation regulation efficiency of the mutant. Indeed, simulations of the unbound riboswitch show that G17 frequently stacks with base 7, while base 8 is stabilized towards the binding site in a way that it may interfere with the conformational selection mechanism and decrease riboswitch regulatory activity. In the riboswitch complexes, this single-point A to G mutation disrupts a strong hydrogen bond between nucleotides 5 and 17 and, instead, a new hydrogen bond between residue 17 and neomycin is created. This change forces neomycin to occupy a slightly shifted position in the binding pocket, which increases neomycin flexibility. Our simulations of the U14C mutation suggest that the riboswitch complex with neomycin is more stable if cytosine 14 is protonated. A hydrogen bond between the RNA phosphate and protonated cytosine appears as the stabilizing factor. Also, based on the cell-free translation assay and isothermal titration calorimetry experiments, mutations of nucleotides 14 and 15 affect only slightly the riboswitch ability to bind the ligand and its activity. Indeed, the simulation of the unbound U15A mutant suggests conformations preformed for ligand binding, which may explain slightly higher regulatory activity of this mutant. Overall, our results corroborate the in vivo and in vitro experiments on the N1 riboswitch-neomycin system, detail the relationship between nucleobase mutations and RNA dynamics, and reveal the conformations playing the major role in the conformational selection mechanism.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,RIKEN Cluster for Pioneering Research (CPR), Wako, Japan.,RIKEN Center for Computational Science, Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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11
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Brunner JS, Vogel A, Lercher A, Caldera M, Korosec A, Pühringer M, Hofmann M, Hajto A, Kieler M, Garrido LQ, Kerndl M, Kuttke M, Mesteri I, Górna MW, Kulik M, Dominiak PM, Brandon AE, Estevez E, Egan CL, Gruber F, Schweiger M, Menche J, Bergthaler A, Weichhart T, Klavins K, Febbraio MA, Sharif O, Schabbauer G. The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nat Metab 2020; 2:1427-1442. [PMID: 33199895 DOI: 10.1038/s42255-020-00311-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/09/2020] [Indexed: 12/25/2022]
Abstract
Adipose tissue macrophages (ATMs) display tremendous heterogeneity depending on signals in their local microenvironment and contribute to the pathogenesis of obesity. The phosphoinositide 3-kinase (PI3K) signalling pathway, antagonized by the phosphatase and tensin homologue (PTEN), is important for metabolic responses to obesity. We hypothesized that fluctuations in macrophage-intrinsic PI3K activity via PTEN could alter the trajectory of metabolic disease by driving distinct ATM populations. Using mice harbouring macrophage-specific PTEN deletion or bone marrow chimeras carrying additional PTEN copies, we demonstrate that sustained PI3K activity in macrophages preserves metabolic health in obesity by preventing lipotoxicity. Myeloid PI3K signalling promotes a beneficial ATM population characterized by lipid uptake, catabolism and high expression of the scavenger macrophage receptor with collagenous structure (MARCO). Dual MARCO and myeloid PTEN deficiencies prevent the generation of lipid-buffering ATMs, reversing the beneficial actions of elevated myeloid PI3K activity in metabolic disease. Thus, macrophage-intrinsic PI3K signalling boosts metabolic health by driving ATM programmes associated with MARCO-dependent lipid uptake.
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Affiliation(s)
- Julia S Brunner
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Andrea Vogel
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael Caldera
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Max Perutz Laboratories, Vienna, Austria
| | - Ana Korosec
- Skin and Endothelium Research Division, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marlene Pühringer
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Melanie Hofmann
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Alexander Hajto
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Markus Kieler
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Lucia Quemada Garrido
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Martina Kerndl
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Mario Kuttke
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | | | - Maria W Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Amanda E Brandon
- Insulin Action and Energy Metabolism Laboratory, Division of Diabetes & Metabolism, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emma Estevez
- Cellular & Molecular Metabolism Laboratory, Division of Diabetes & Metabolism, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Casey L Egan
- Cellular & Molecular Metabolism Laboratory, Division of Diabetes & Metabolism, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Florian Gruber
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Martina Schweiger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Max Perutz Laboratories, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Weichhart
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Kristaps Klavins
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre, Riga Technical University, Riga, Latvia
| | - Mark A Febbraio
- Cellular & Molecular Metabolism Laboratory, Division of Diabetes & Metabolism, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Omar Sharif
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria.
| | - Gernot Schabbauer
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria.
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12
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Kulik M, Mori T, Sugita Y, Trylska J. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Res 2019; 46:9960-9970. [PMID: 30239867 PMCID: PMC6212780 DOI: 10.1093/nar/gky833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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Affiliation(s)
- Marta Kulik
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Yuji Sugita
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure 2018; 27:161-174.e3. [PMID: 30344106 DOI: 10.1016/j.str.2018.09.004] [Citation(s) in RCA: 14] [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: 02/28/2018] [Revised: 06/22/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023]
Abstract
Flexible fitting is a powerful technique to build the 3D structures of biomolecules from cryoelectron microscopy (cryo-EM) density maps. One popular method is a cross-correlation coefficient-based approach, where the molecular dynamics (MD) simulation is carried out with the biasing potential that includes the cross-correlation coefficient between the experimental and simulated density maps. Here, we propose efficient parallelization schemes for the calculation of the cross-correlation coefficient to accelerate flexible fitting. Our schemes are tested for small, medium, and large biomolecules using CPU and hybrid CPU + GPU architectures. The scheme for the atomic decomposition MD is suitable for small proteins such as Ca2+-ATPase with the all-atom Go model, while that for the domain decomposition MD is better for larger systems such as ribosome with the all-atom Go or the all-atom explicit solvent models. Our methods allow flexible fitting for various biomolecules with reasonable computational cost. This approach also connects high-resolution structure refinements with investigation of protein structure-function relationship.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Physics, Graduate School of Science, and Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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Kulik M, Kołodyńska D, Bayramov A, Drozdziel A, Olejniczak A, Żuk J. Dielectric functions, chemical and atomic compositions of the near surface layers of implanted GaAs by In + ions. Spectrochim Acta A Mol Biomol Spectrosc 2018; 198:222-231. [PMID: 29547824 DOI: 10.1016/j.saa.2018.02.032] [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] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/30/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
The surfaces of (100) GaAs were irradiated with In+ ions. The implanted samples were isobaric annealed at 800°C and then of dielectric function, the surface atomic concentrations of atoms and also the chemical composition of the near surface layers in these implanted semiconductor samples were obtained. The following investigation methods were used: spectroscopic ellipsometry (SE), Rutherford backscattering spectrometry analyses (RBSA) and X-ray photoelectron spectroscopy (XPS) in the study of the above mentioned quantities, respectively. The change of the shape spectra of the dielectric functions at about 3.0eV phonon energy, diffusion of In+ ions as well as chemical composition changes were observed after ion implantation and the thermal treatment. Due to displacement of Ga ions from GaAs by the In+ ions the new chemical compound InAs was formed. The relative amounts Ga2O3 and As2O3 ratio increase in the native oxide layers with the fluences increase after the thermal treatment of the samples. Additionally, it was noticed that the quantities of InO2 increase with the increasing values of the irradiated ions before thermal treatment.
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Affiliation(s)
- M Kulik
- Joint Institute for Nuclear Research, St. 6 Joliot-Curie, Dubna, Moscow 141980, Russia; Institute of Physics, Maria Curie-Skłodowska University, Sq. 1 Maria Curie-Skłodowska, 20-031 Lublin, Poland.
| | - D Kołodyńska
- Faculty of Chemistry, Maria Curie-Skłodowska University, Sq. 2 Maria Curie-Skłodowska, 20-031 Lublin, Poland
| | - A Bayramov
- Institute of Physics, ANAS, AZ-1143 Baku, Azerbaijan
| | - A Drozdziel
- Institute of Physics, Maria Curie-Skłodowska University, Sq. 1 Maria Curie-Skłodowska, 20-031 Lublin, Poland
| | - A Olejniczak
- Faculty of Chemistry, Nicolaus Copernicus University, St. Gagarina 7, Toruń, Poland
| | - J Żuk
- Institute of Physics, Maria Curie-Skłodowska University, Sq. 1 Maria Curie-Skłodowska, 20-031 Lublin, Poland
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Jasiński M, Kulik M, Wojciechowska M, Stolarski R, Trylska J. Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PLoS One 2018; 13:e0191138. [PMID: 29351348 PMCID: PMC5774723 DOI: 10.1371/journal.pone.0191138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2’-O-methylated (2’-O-Me) oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined. We have analyzed three 2’-O-Me oligoribonucleotides designed to hybridize with the models of the prokaryotic rRNA containing two neighboring aminoglycoside binding pockets. One pocket is the paromomycin/kanamycin binding site corresponding to the decoding site in the small ribosomal subunit and the other one is the close-by hygromycin B binding site whose dynamics has not been previously reported. Molecular dynamics (MD) simulations, as well as isothermal titration calorimetry, gel electrophoresis and spectroscopic studies have shown that the eukaryotic rRNA model is less conformationally stable (in terms of hydrogen bonds and stacking interactions) than the corresponding prokaryotic one. In MD simulations of the eukaryotic construct, the nucleotide U1498, which plays an important role in correct positioning of mRNA during translation, is flexible and spontaneously flips out into the solvent. In solution studies, the 2’-O-Me oligoribonucleotides did not interact with the double stranded rRNA models but all formed stable complexes with the single-stranded prokaryotic target. 2’-O-Me oligoribonucleotides with one and two mismatches bound less tightly to the eukaryotic target. This shows that at least three mismatches between the 2’-O-Me oligoribonucleotide and eukaryotic rRNA are required to ensure target selectivity. The results also suggest that, in the ribosome environment, the strand invasion is the preferred binding mode of 2’-O-Me oligoribonucleotides targeting the aminoglycoside binding sites in 16S rRNA.
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Affiliation(s)
- Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Ryszard Stolarski
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- * E-mail:
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Murphy M, Barry F, Leschke C, Vaughan B, Gentili C, O'Dea J, Ogourtsov V, Rafiq Q, Ochs J, Kulik M, Koenig N. The AUTOSTEM platform for closed manufacture of bone marrow-derived mesenchymal stromal cells using a closed, scalable and automated robotic system. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kulik M, Markowska-Zagrajek A, Wojciechowska M, Grzela R, Wituła T, Trylska J. Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target. Biochimie 2017; 138:32-42. [PMID: 28396015 DOI: 10.1016/j.biochi.2017.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 03/03/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
A fragment of 23S ribosomal RNA (nucleotides 1906-1924 in E. coli), termed Helix 69, forms a hairpin that is essential for ribosome function. Helix 69 forms a conformationally flexible inter-subunit connection with helix 44 of 16S ribosomal RNA, and the nucleotide A1913 of Helix 69 influences decoding accuracy. Nucleotides U1911 and U1917 are post-transcriptionally modified with pseudouridines (Ψ) and U1915 with 3-methyl-Ψ. We investigated Helix 69 as a target for a complementary synthetic oligonucleotide - peptide nucleic acid (PNA). We determined thermodynamic properties of Helix 69 and its complexes with PNA and tested the performance of PNA targeted at Helix 69 in inhibiting translation in cell-free extracts and growth of E. coli cells. First, we examined the interactions of a PNA oligomer complementary to the G1907-A1919 fragment of Helix 69 with the sequences corresponding to human and bacterial species (with or without pseudouridine modifications). PNA invades the Helix 69 hairpin creating stable complexes and PNA binding to the pseudouridylated bacterial sequence is stronger than to Helix 69 without any modifications. Second, we confirmed the binding of PNA to 23S rRNA and 70S ribosomes. Third, we verified the efficiency of translation inhibition of these PNA oligomers in the cell-free translation/transcription E. coli system, which were in a similar range as tetracycline. Next, we confirmed that PNA conjugated to the (KFF)3K transporter peptide inhibited E. coli growth in micromolar concentrations. Overall, targeting Helix 69 with PNA or other sequence-specific oligomers could be a promising way to inhibit bacterial translation.
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Affiliation(s)
- Marta Kulik
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Agnieszka Markowska-Zagrajek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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Kulik M, Nedelcu C, Martin F, Lebdai S, Rousselet MC, Azzouzi AR, Aubé C. Post-treatment MRI aspects of photodynamic therapy for prostate cancer. Insights Imaging 2014; 5:697-713. [PMID: 25288529 PMCID: PMC4263801 DOI: 10.1007/s13244-014-0359-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Photodynamic therapy is a new focal therapy for prostate cancer. METHODS In this technique, a photosensitising agent is introduced intravenously, then activated by local laser illumination to induce tumour necrosis. Treatment efficacy is assessed by magnetic resonance imaging (MRI). RESULTS AND CONCLUSIONS We illustrate specific post-treatment MRI aspects at early and late follow-up with pathological correlations. TEACHING POINTS • Dynamic phototherapy is a new and promising focal therapy for prostate cancer. • One-week MRI shows increased volume of the treated lobe and large, homogeneous necrosis area. • Six-month MRI shows significant changes of the prostate shape and signal. • Six-month MRI becomes "base line" appearance for further follow-up or monitoring.
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Affiliation(s)
- M Kulik
- Department of Radiology, CHU Angers, 4 rue Larrey, 49100, Angers, France,
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Kulik M, Pazio A, Wozniak K. Bis(l-serinium) oxalate dihydrate: polymorph II. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o1667-8. [PMID: 24454102 PMCID: PMC3884326 DOI: 10.1107/s160053681302727x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 06/13/2013] [Accepted: 10/03/2013] [Indexed: 11/22/2022]
Abstract
A corrected and improved structure of the polymorph II of 2C3H8NO3+·C2O42−·2H2O, based on single-crystal data, is presented. The structure is refined with anisotropic displacement parameters for all non-H atoms and all H atoms are located. Due to the charged moieties, the structure is classified as a molecular salt. Intermolecular O—H⋯O−, O—H⋯O and N+—H⋯O−hydrogen bonds link the components of the structure. The l-serinium cations and oxalate anions form a network of channels in [100] direction, filled with the water molecules of crystallization. The dihedral angle between the CO2 units of the oxalate dianion is 10.2 (3)°
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Affiliation(s)
- Marta Kulik
- Chemistry Department, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland, and, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warszawa, Poland
| | - Aleksandra Pazio
- Chemistry Department, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
| | - Krzysztof Wozniak
- Chemistry Department, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
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Hagenmeyer EG, Gothe H, Landgraf W, Kulik M, Schiffhorst G, Häussler B. Ressourcen-Inanspruchnahme und Kosten der Behandlung von Typ-2-Diabetikern unter Insulin-glargin- oder Insulindetemir-Therapie (LIVE-KK): Analyse von Krankenkassen-Routinedaten mittels Propensity Score Matching. Gesundh ökon Qual manag 2010. [DOI: 10.1055/s-0028-1110023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Urbaniak M, Król H, Zawadzka B, Kulik M, Frankiewicz A, Łyczyński A, Pospiech E, Wasilewski Z. Effect of soyabean meal, rapeseed meal and
extruded field bean seeds on duodenal amino acids
supply in sheep. J Anim Feed Sci 2001. [DOI: 10.22358/jafs/67997/2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Urbaniak M, Gut A, Król H, Zawadzka B, Kulik M, Frankiewicz A, Łyczyński A. Supplementation of mixed roughage-based diet with
rumen protected methionine for lactating goats. J Anim Feed Sci 2001. [DOI: 10.22358/jafs/70027/2001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Urbaniak M, Frankiewicz A, Łyczyński A, Mroczyk W, Wasilewski Z, Zawadzka B, Kulik M. Tissue protein and energy deposition in White-headed Mutton sheep x Polish Merino crossbred rams fed diets with different energy values. J Anim Feed Sci 2001. [DOI: 10.22358/jafs/68269/2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sznitowska M, Janicki S, Gajewska M, Kulik M. Investigation of diazepam lipospheres based on Witepsol and lecithin intended for oral or rectal delivery. Acta Pol Pharm 2000; 57:61-4. [PMID: 10846799] [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] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Diazepam was incorporated in lipospheres prepared by high pressure homogenization of melted Witepsol (10%) dispersed in aqueous lecithin (2.4%). Diazepam content was 0.4% and more than 98% of the dose was found to be encapsulated in the lipospheres. Although the initial mean particle size was 0.3 micron, the liposhperes agglomerated during storage and this phenomenon was not eliminated by increasing lecithin concentration to 4% or incorporation of oleic acid (0.1%) and co-surfactants, polysorbate 80 (0.5%) or poloxamer (up to 6%). The formulation was not able to mask effectively bitter taste of diazepam, even when lipids of higher melting temperature, namely glyceryl tripalmitate or stearic acid, were introduced.
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Affiliation(s)
- M Sznitowska
- Department of Pharmaceutical Technology, Medical University of Gdańsk, Poland
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Desroys du Roure F, Louvet C, de Gramont A, Varette C, Demuynck B, Beerblock K, Kulik M. [Detection of ovarian adenocarcinoma in the occasion of cerebrovascular complication associated with consumption coagulopathy]. Rev Med Interne 1994; 15:48-51. [PMID: 8052754 DOI: 10.1016/s0248-8663(05)82130-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [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: 01/28/2023]
Abstract
A 58 year-old woman was hospitalized for an hemorrhagic stroke, associated with a consumption's coagulopathy, related to a stage Ic ovarian carcinoma. After surgery and chemotherapy, hemostasic disorders disappeared. The same disorders occurred at tumoral relapse. Relationships between thrombotic or haemorrhagic manifestations and neoplasms are discussed, with emphasis on singularity of such phenomenon in ovarian carcinoma.
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Affiliation(s)
- F Desroys du Roure
- Service de médecine interne-oncologie, hôpital Saint-Antoine, Paris, France
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Kuduk R, Kulik M, Maczka D, Pyszniak K, Żuk J. Depth Profile Measurements of Ions Implanted in Semiconductor Materials by Particle Induced Photon Emission. ACTA ACUST UNITED AC 1989. [DOI: 10.1002/pssa.2211120247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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