1
|
Jurczak P, Fayad N, Benard M, Czaplewska P, Hildebrandt N. Monomer-Dimer Equilibrium of Human Cystatin C During Internalization Into Cancer Cells. Chembiochem 2024; 25:e202400226. [PMID: 38761032 DOI: 10.1002/cbic.202400226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/26/2024] [Accepted: 05/17/2024] [Indexed: 05/20/2024]
Abstract
Human cystatin C (hCC) is a physiologically important protein that serves as intra- and extracellular cysteine proteinase inhibitor in homeostasis. However, in pathological states it dimerizes and further oligomerizes accumulating into a toxic amyloid. HCC forms an active monomer in the extracellular space and becomes an inactive dimer when internalized in cellular organelles. However, hCC cell penetration and its oligomeric state during this process are not well understood. To determine if and how the oligomeric state influences hCC transmembrane migration, we investigated the internalization of the hCC wild type protein as well as three different mutants, which exclusively exist in the monomeric or multimeric state into HeLa cells via confocal fluorescence microscopy. Our results showed that the preferred pathway was endocytosis and that the oligomeric state did not significantly influence the internalization because both monomeric and dimeric hCC migrated into HeLa cells. Considering the differences of the active monomeric and the passive dimeric states of hCC, our findings contribute to a better understanding of the intra and extra cellular functions of hCC and their interaction with cysteine proteases.
Collapse
Affiliation(s)
- Przemyslaw Jurczak
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, Gdańsk, 80-307, Poland
- Laboratoire COBRA (UMR6014 & FR3038), Université de Rouen Normandie, CNRS, INSA, Normandie Université, Rouen, 76000, France
| | - Nour Fayad
- Laboratoire COBRA (UMR6014 & FR3038), Université de Rouen Normandie, CNRS, INSA, Normandie Université, Rouen, 76000, France
| | - Magalie Benard
- PRIMACEN, Univ Rouen Normandie, INSERM, CNRS, HeRacLeS US51 UAR2026, Rouen, 76000, France
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, Gdańsk, 80-307, Poland
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, L8S4 L7, Canada
| |
Collapse
|
2
|
Zhukov I, Sikorska E, Orlikowska M, Górniewicz-Lorens M, Kepczynski M, Jurczak P. DPPA as a Potential Cell Membrane Component Responsible for Binding Amyloidogenic Protein Human Cystatin C. Molecules 2024; 29:3446. [PMID: 39124852 PMCID: PMC11313537 DOI: 10.3390/molecules29153446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
A phospholipid bilayer is a typical structure that serves crucial functions in various cells and organelles. However, it is not unusual for it to take part in pathological processes. The cell membrane may be a binding target for amyloid-forming proteins, becoming a factor modulating the oligomerization process leading to amyloid deposition-a hallmark of amyloidogenic diseases-e.g., Alzheimer's disease. The information on the mechanisms governing the oligomerization influenced by the protein-membrane interactions is scarce. Therefore, our study aims to describe the interactions between DPPA, a cell membrane mimetic, and amyloidogenic protein human cystatin C. Circular dichroism spectroscopy and differential scanning calorimetry were used to monitor (i) the secondary structure of the human cystatin C and (ii) the phase transition temperature of the DPPA, during the protein-membrane interactions. NMR techniques were used to determine the protein fragments responsible for the interactions, and molecular dynamics simulations were applied to provide a molecular structure representing the interaction. The obtained data indicate that the protein interacts with DPPA, submerging itself into the bilayer via the AS region. Additionally, the interaction increases the content of α-helix within the protein's secondary structure and stabilizes the whole molecule against denaturation.
Collapse
Affiliation(s)
- Igor Zhukov
- Laboratory of Biological NMR, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Marta Orlikowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Magdalena Górniewicz-Lorens
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland; (M.G.-L.); (M.K.)
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Profesora Stanisława Łojasiewicza 11, 30-348 Krakow, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland; (M.G.-L.); (M.K.)
| | - Przemyslaw Jurczak
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdansk, 80-307 Gdansk, Poland
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi 351-0198, Saitama, Japan
| |
Collapse
|
3
|
Żyła A, Martel A, Jurczak P, Moliński A, Szymańska A, Kozak M. Human cystatin C induces the disaggregation process of selected amyloid beta peptides: a structural and kinetic view. Sci Rep 2023; 13:20833. [PMID: 38012338 PMCID: PMC10682421 DOI: 10.1038/s41598-023-47514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD) and various types of amyloidosis, are incurable; therefore, understanding the mechanisms of amyloid decomposition is crucial to develop an effective drug against them for future therapies. It has been reported that one out of three people over the age of 85 are suffering from dementia as a comorbidity to AD. Amyloid beta (Aβ), the hallmark of AD, transforms structurally from monomers into β-stranded aggregates (fibrils) via multiple oligomeric states. Astrocytes in the central nervous system secrete the human cystatin C protein (HCC) in response to various proteases and cytokines. The codeposition of Aβ and HCC in the brains of patients with AD led to the hypothesis that cystatin C is implicated in the disease process. In this study, we investigate the intermolecular interactions between different atomic structures of fibrils formed by Aβ peptides and HCC to understand the pathological aggregation of these polypeptides into neurotoxic oligomers and then amyloid plaques. To characterize the interactions between Aβ and HCC, we used a complementary approach based on the combination of small-angle neutron scattering analysis, atomic force microscopy and computational modelling, allowing the exploration of the structures of multicomponent protein complexes. We report here an optimized protocol to study that interaction. The results show a dependency of the sequence length of the Aβ peptide on the ability of the associated HCC to disaggregate it.
Collapse
Affiliation(s)
- Adriana Żyła
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland
| | - Anne Martel
- Large Scale Structures, ILL Neutrons for Society, Institute Laue-Langevin, Grenoble, France
| | - Przemysław Jurczak
- Laboratory of Medical Chemistry, Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Augustyn Moliński
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland
| | - Aneta Szymańska
- Laboratory of Medical Chemistry, Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland.
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Kraków, Poland.
| |
Collapse
|
4
|
Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| |
Collapse
|
5
|
Wojciechowska D, Taube M, Rucińska K, Maksim J, Kozak M. Oligomerization of Human Cystatin C—An Amyloidogenic Protein: An Analysis of Small Oligomeric Subspecies. Int J Mol Sci 2022; 23:ijms232113441. [PMID: 36362228 PMCID: PMC9656228 DOI: 10.3390/ijms232113441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Human cystatin C (HCC), an amyloidogenic protein, forms dimers and higher oligomers (trimers, tetramers and donut like large oligomers) via a domain-swapping mechanism. The aim of this study was the characterization of the HCC oligomeric states observed within the pH range from 2.2 to 10.0 and also in conditions promoting oligomerization. The HCC oligomeric forms obtained in different conditions were characterized using size exclusion chromatography, dynamic light scattering and small-angle X-ray scattering. The marked ability of HCC to form tetramers at low pH (2.3 or 3.0) and dimers at pH 4.0–5.0 was observed. HCC remains monomeric at pH levels above 6.0. Based on the SAXS data, the structure of the HCC tetramer was proposed. Changes in the environment (from acid to neutral) induced a breakdown of the HCC tetramers to dimers. The tetrameric forms of human cystatin C are formed by the association of the dimers without a domain-swapping mechanism. These observations were confirmed by their dissociation to dimers at pH 7.4.
Collapse
Affiliation(s)
- Daria Wojciechowska
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Karolina Rucińska
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Joanna Maksim
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, 30-392 Kraków, Poland
- Correspondence:
| |
Collapse
|
6
|
Sagar A, Bernadó P. Disentangling polydisperse biomolecular systems by Chemometrics decomposition of SAS data. Methods Enzymol 2022; 677:531-555. [DOI: 10.1016/bs.mie.2022.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
7
|
Jurczak P, Szutkowski K, Lach S, Jurga S, Czaplewska P, Szymanska A, Zhukov I. DMPC Phospholipid Bilayer as a Potential Interface for Human Cystatin C Oligomerization: Analysis of Protein-Liposome Interactions Using NMR Spectroscopy. MEMBRANES 2020; 11:membranes11010013. [PMID: 33374166 PMCID: PMC7824490 DOI: 10.3390/membranes11010013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022]
Abstract
Studies revolving around mechanisms responsible for the development of amyloid-based diseases lay the foundations for the recognition of molecular targets of future to-be-developed treatments. However, the vast number of peptides and proteins known to be responsible for fibril formation, combined with their complexity and complexity of their interactions with various cellular components, renders this task extremely difficult and time-consuming. One of these proteins, human cystatin C (hCC), is a well-known and studied cysteine-protease inhibitor. While being a monomer in physiological conditions, under the necessary stimulus—usually a mutation, it tends to form fibrils, which later participate in the disease development. This process can potentially be regulated (in several ways) by many cellular components and it is being hypothesized that the cell membrane might play a key role in the oligomerization pathway. Studies involving cell membranes pose several difficulties; therefore, an alternative in the form of membrane mimetics is a very attractive solution. Here, we would like to present the first study on hCC oligomerization under the influence of phospholipid liposomes, acting as a membrane mimetic. The protein–mimetic interactions are studied utilizing circular dichroism, nuclear magnetic resonance, and size exclusion chromatography.
Collapse
Affiliation(s)
- Przemyslaw Jurczak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.J.); (S.L.); (A.S.)
| | - Kosma Szutkowski
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland; (K.S.); (S.J.)
| | - Slawomir Lach
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.J.); (S.L.); (A.S.)
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland; (K.S.); (S.J.)
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG & MUG, University of Gdańsk, Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland;
| | - Aneta Szymanska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.J.); (S.L.); (A.S.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106 Warszawa, Poland
- Correspondence: ; Tel.: +48-22-592-2038
| |
Collapse
|
8
|
Mital M, Szutkowski K, Bossak-Ahmad K, Skrobecki P, Drew SC, Poznański J, Zhukov I, Frączyk T, Bal W. The Palladium(II) Complex of A β4-16 as Suitable Model for Structural Studies of Biorelevant Copper(II) Complexes of N-Truncated Beta-Amyloids. Int J Mol Sci 2020; 21:E9200. [PMID: 33276669 PMCID: PMC7731285 DOI: 10.3390/ijms21239200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
The Aβ4-42 peptide is a major beta-amyloid species in the human brain, forming toxic aggregates related to Alzheimer's Disease. It also strongly chelates Cu(II) at the N-terminal Phe-Arg-His ATCUN motif, as demonstrated in Aβ4-16 and Aβ4-9 model peptides. The resulting complex resists ROS generation and exchange processes and may help protect synapses from copper-related oxidative damage. Structural characterization of Cu(II)Aβ4-x complexes by NMR would help elucidate their biological function, but is precluded by Cu(II) paramagneticism. Instead we used an isostructural diamagnetic Pd(II)-Aβ4-16 complex as a model. To avoid a kinetic trapping of Pd(II) in an inappropriate transient structure, we designed an appropriate pH-dependent synthetic procedure for ATCUN Pd(II)Aβ4-16, controlled by CD, fluorescence and ESI-MS. Its assignments and structure at pH 6.5 were obtained by TOCSY, NOESY, ROESY, 1H-13C HSQC and 1H-15N HSQC NMR experiments, for natural abundance 13C and 15N isotopes, aided by corresponding experiments for Pd(II)-Phe-Arg-His. The square-planar Pd(II)-ATCUN coordination was confirmed, with the rest of the peptide mostly unstructured. The diffusion rates of Aβ4-16, Pd(II)-Aβ4-16 and their mixture determined using PGSE-NMR experiment suggested that the Pd(II) complex forms a supramolecular assembly with the apopeptide. These results confirm that Pd(II) substitution enables NMR studies of structural aspects of Cu(II)-Aβ complexes.
Collapse
Affiliation(s)
- Mariusz Mital
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Kosma Szutkowski
- NanoBioMedical Centre, Adam Mickiewicz University, 61-614 Poznań, Poland;
| | - Karolina Bossak-Ahmad
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Piotr Skrobecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Simon C. Drew
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Tomasz Frączyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warszawa, Poland; (M.M.); (K.B.-A.); (P.S.); (S.C.D.); (J.P.)
| |
Collapse
|
9
|
Kolonko M, Bystranowska D, Taube M, Kozak M, Bostock M, Popowicz G, Ożyhar A, Greb-Markiewicz B. The intrinsically disordered region of GCE protein adopts a more fixed structure by interacting with the LBD of the nuclear receptor FTZ-F1. Cell Commun Signal 2020; 18:180. [PMID: 33153474 PMCID: PMC7643343 DOI: 10.1186/s12964-020-00662-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
The Drosophila melanogaster Germ cell-expressed protein (GCE) is a paralog of the juvenile hormone (JH) receptor - Methoprene tolerant protein (MET). Both proteins mediate JH function, preventing precocious differentiation during D. melanogaster development. Despite that GCE and MET are often referred to as equivalent JH receptors, their functions are not fully redundant and show tissue specificity. Both proteins belong to the family of bHLH-PAS transcription factors. The similarity of their primary structure is limited to defined bHLH and PAS domains, while their long C-terminal fragments (GCEC, METC) show significant differences and are expected to determine differences in GCE and MET protein activities. In this paper we present the structural characterization of GCEC as a coil-like intrinsically disordered protein (IDP) with highly elongated and asymmetric conformation. In comparison to previously characterized METC, GCEC is less compacted, contains more molecular recognition elements (MoREs) and exhibits a higher propensity for induced folding. The NMR shifts perturbation experiment and pull-down assay clearly demonstrated that the GCEC fragment is sufficient to form an interaction interface with the ligand binding domain (LBD) of the nuclear receptor Fushi Tarazu factor-1 (FTZ-F1). Significantly, these interactions can force GCEC to adopt more fixed structure that can modulate the activity, structure and functions of the full-length receptor. The discussed relation of protein functionality with the structural data of inherently disordered GCEC fragment is a novel look at this protein and contributes to a better understanding of the molecular basis of the functions of the C-terminal fragments of the bHLH-PAS family. Video abstract.
Collapse
Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
| | - Mark Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Grzegorz Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
| |
Collapse
|
10
|
Deng D, Zhang L, Dong M, Samuel RE, Ofori-Boadu A, Lamssali M. Radioactive waste: A review. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:1818-1825. [PMID: 32860717 DOI: 10.1002/wer.1442] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
The reviewed papers presented here provide a general overview of worldwide radioactive waste-related studies conducted in 2019. The current review includes studies related to safety assessments, decommission and decontamination of nuclear facilities, fusion facilities, and transportation. Further, the review highlights radioactive wastewater decontamination, management solutions for the final disposal of low- and high-level radioactive wastes (LLRW and HLRW), interim storage and final disposal options for spent fuel (SF), and tritiated wastes, with a focus on environmental impacts due to the mobility of radionuclides in the ecosystem, water and soil along with other research progress made in the management of radioactive waste. PRACTITIONER POINTS: The release of radionuclides and their subsequent fate and transport in the environment poses public health concern and has stimulated recent research on the waste management techniques. Seeking a safe and environmental-friendly solution is the current trend for existing and projected inventories of radioactive waste. Significant progress in the field of geological disposal of radioactive waste has been made in the last two decades.
Collapse
Affiliation(s)
- Dongyang Deng
- Department of Built Environment, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Lifeng Zhang
- Department of Nanoengineering, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Ming Dong
- Department of Chemistry, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Raymond E Samuel
- Department of Biology, Center for Outreach in Alzheimer's Aging and Community Health (COAACH), North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Andrea Ofori-Boadu
- Department of Built Environment, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Mehdi Lamssali
- Department of Built Environment, North Carolina A&T State University, Greensboro, North Carolina, USA
| |
Collapse
|
11
|
Chrabąszczewska M, Sieradzan AK, Rodziewicz-Motowidło S, Grubb A, Dobson CM, Kumita JR, Kozak M. Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers. Int J Mol Sci 2020; 21:ijms21165860. [PMID: 32824145 PMCID: PMC7461555 DOI: 10.3390/ijms21165860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Human cystatin C (HCC), a cysteine-protease inhibitor, exists as a folded monomer under physiological conditions but has the ability to self-assemble via domain swapping into multimeric states, including oligomers with a doughnut-like structure. The structure of the monomeric HCC has been solved by X-ray crystallography, and a covalently linked version of HCC (stab-1 HCC) is able to form stable oligomeric species containing 10-12 monomeric subunits. We have performed molecular modeling, and in conjunction with experimental parameters obtained from atomic force microscopy (AFM), transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) measurements, we observe that the structures are essentially flat, with a height of about 2 nm, and the distance between the outer edge of the ring and the edge of the central cavity is ~5.1 nm. These dimensions correspond to the height and diameter of one stab-1 HCC subunit and we present a dodecamer model for stabilized cystatin C oligomers using molecular dynamics simulations and experimentally measured parameters. Given that oligomeric species in protein aggregation reactions are often transient and very highly heterogeneous, the structural information presented here on these isolated stab-1 HCC oligomers may be useful to further explore the physiological relevance of different structural species of cystatin C in relation to protein misfolding disease.
Collapse
Affiliation(s)
- Magdalena Chrabąszczewska
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland;
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (A.K.S.); (S.R.-M.)
| | | | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden;
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Janet R. Kumita
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
- Correspondence: (J.R.K.); (M.K.)
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland;
- Correspondence: (J.R.K.); (M.K.)
| |
Collapse
|
12
|
Maszota-Zieleniak M, Jurczak P, Orlikowska M, Zhukov I, Borek D, Otwinowski Z, Skowron P, Pietralik Z, Kozak M, Szymańska A, Rodziewicz-Motowidło S. NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution. FEBS J 2019; 287:361-376. [PMID: 31330077 DOI: 10.1111/febs.15010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/14/2019] [Accepted: 07/19/2019] [Indexed: 02/02/2023]
Abstract
Human cystatin C (hCC), a member of the superfamily of papain-like cysteine protease inhibitors, is the most widespread cystatin in human body fluids. This small protein, in addition to its physiological function, is involved in various diseases, including cerebral amyloid angiopathy, cerebral hemorrhage, stroke, and dementia. Physiologically active hCC is a monomer. However, all structural studies based on crystallization led to the dimeric structure formed as a result of a three-dimensional exchange of the protein domains (3D domain swapping). The monomeric structure was obtained only for hCC variant V57N and for the protein stabilized by an additional disulfide bridge. With this study, we extend the number of models of monomeric hCC by an additional hCC variant with a single amino acid substitution in the flexible loop L1. The V57G variant was chosen for the X-ray and NMR structural analysis due to its exceptional conformational stability in solution. In this work, we show for the first time the structural and dynamics studies of human cystatin C variant in solution. We were also able to compare these data with the crystal structure of the hCC V57G and with other cystatins. The overall cystatin fold is retained in the solute form. Additionally, structural information concerning the N terminus was obtained during our studies and presented for the first time. DATABASE: Crystallographic structure: structural data are available in PDB databases under the accession number 6ROA. NMR structure: structural data are available in PDB and BMRB databases under the accession numbers 6RPV and 34399, respectively.
Collapse
Affiliation(s)
| | | | | | - Igor Zhukov
- NanoBioMedical Centre, Adam Mickiewicz University, Poznan, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dominika Borek
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Piotr Skowron
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Adam Mickiewicz University, Poznan, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University, Poznan, Poland
| | | | | |
Collapse
|
13
|
Gielnik M, Pietralik Z, Zhukov I, Szymańska A, Kwiatek WM, Kozak M. PrP (58-93) peptide from unstructured N-terminal domain of human prion protein forms amyloid-like fibrillar structures in the presence of Zn 2+ ions. RSC Adv 2019; 9:22211-22219. [PMID: 35519468 PMCID: PMC9066832 DOI: 10.1039/c9ra01510h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/07/2019] [Indexed: 12/12/2022] Open
Abstract
Many transition metal ions modulate the aggregation of different amyloid peptides. Substoichiometric zinc concentrations can inhibit aggregation, while an excess of zinc can accelerate the formation of cytotoxic fibrils. In this study, we report the fibrillization of the octarepeat domain to amyloid-like structures. Interestingly, this self-assembling process occurred only in the presence of Zn(ii) ions. The formed peptide aggregates are able to bind amyloid specific dyes thioflavin T and Congo red. Atomic force microscopy and transmission electron microscopy revealed the formation of long, fibrillar structures. X-ray diffraction and Fourier transform infrared spectroscopy studies of the formed assemblies confirmed the presence of cross-β structure. Two-component analysis of synchrotron radiation SAXS data provided the evidence for a direct decrease in monomeric peptide species content and an increase in the fraction of aggregates as a function of Zn(ii) concentration. These results could shed light on Zn(ii) as a toxic agent and on the metal ion induced protein misfolding in prion diseases.
Collapse
Affiliation(s)
- Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences PL 02-106 Warszawa Poland
- NanoBioMedical Centre, Adam Mickiewicz University PL 61-614 Poznań Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, Gdańsk University PL 80-308 Gdańsk Poland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics Polish Academy of Sciences PL 31-342 Krakow Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
- Joint Laboratory for SAXS Studies, Faculty of Physics, Adam Mickiewicz University PL 61-614 Poznań Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University PL 30-392 Kraków Poland
| |
Collapse
|
14
|
Garman EF, Weik M. X-ray radiation damage to biological samples: recent progress. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:907-911. [PMID: 31274412 DOI: 10.1107/s1600577519009408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 05/20/2023]
Abstract
With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| |
Collapse
|