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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: 10] [Impact Index Per Article: 2.0] [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.
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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
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Tu M, Huang Y, Li HL, Gao ZH. The stress caused by nitrite with titanium dioxide nanoparticles under UVA irradiation in human keratinocyte cell. Toxicology 2012; 299:60-8. [DOI: 10.1016/j.tox.2012.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 11/27/2022]
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Rousseau F, Schymkowitz J, Itzhaki LS. Implications of 3D domain swapping for protein folding, misfolding and function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:137-52. [PMID: 22949116 DOI: 10.1007/978-1-4614-3229-6_9] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Three-dimensional domain swapping is the process by which two identical protein chains exchange a part of their structure to form an intertwined dimer or higher-order oligomer. The phenomenon has been observed in the crystal structures of a range of different proteins. In this chapter we review the experiments that have been performed in order to understand the sequence and structural determinants of domain-swapping and these show how the general principles obtained can be used to engineer proteins to domain swap. We discuss the role of domain swapping in regulating protein function and as one possible mechanism of protein misfolding that can lead to aggregation and disease. We also review a number of interesting pathways of macromolecular assembly involving β-strand insertion or complementation that are related to the domain-swapping phenomenon.
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Affiliation(s)
- Frederic Rousseau
- VIB Switch Laboratory, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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Yoshida H, Teraoka M, Yoshihara A, Izumori K, Kamitori S. Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1281-4. [PMID: 22102048 DOI: 10.1107/s1744309111030351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 07/27/2011] [Indexed: 05/26/2023]
Abstract
Acinetobacter sp. L-ribose isomerase (L-RI) catalyzes a reversible isomerization reaction between L-ribose and L-ribulose. To date, information on L-RI remains limited and its amino-acid sequence shows no similarity to those of any known enzymes. Here, recombinant His-tagged L-RI was successfully overexpressed, purified and crystallized. Crystals of His-tagged L-RI were obtained by the hanging-drop vapour-diffusion method at room temperature as two crystal forms which belonged to the monoclinic space group C2, with unit-cell parameters a = 96.60, b = 105.89, c = 71.83 Å, β = 118.16°, and the orthorhombic space group F222, with unit-cell parameters a = 96.44, b = 106.26, c = 117.83 Å. Diffraction data were collected to 3.1 and 2.2 Å resolution, respectively.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Kita-gun, Kagawa 761-0795, Japan
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Abstract
Cystatins, the classical inhibitors of C1 cysteine proteinases, have been extensively studied and reviewed in the literature. Over the last 20 years, however, proteins containing cystatin domains but lacking protease inhibitory activities have been identified, and most likely more will be described in the near future. These proteins together with family 1, 2, and 3 cystatins constitute the cystatin superfamily. Mounting evidence points to the new roles that some members of the superfamily have acquired over the course of their evolution. This review is focused on the roles of cystatins in: 1) tumorigenesis, 2) stabilization of matrix metalloproteinases, 3) glomerular filtration rate, 4) immunomodulation, and 5) neurodegenerative diseases. It is the goal of this review to get as many investigators as possible to take a second look at the cystatin superfamily regarding their potential involvement in serious human ailments.
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Affiliation(s)
- Josiah Ochieng
- Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA.
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Rodziewicz-Motowidło S, Iwaszkiewicz J, Sosnowska R, Czaplewska P, Sobolewski E, Szymańska A, Stachowiak K, Liwo A. The role of the Val57 amino-acid residue in the hinge loop of the human cystatin C. Conformational studies of the beta2-L1-beta3 segments of wild-type human cystatin C and its mutants. Biopolymers 2009; 91:373-83. [PMID: 19137579 DOI: 10.1002/bip.21140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ceruso MA, Weinstein H. Structural mimicry of proline kinks: tertiary packing interactions support local structural distortions. J Mol Biol 2002; 318:1237-49. [PMID: 12083514 DOI: 10.1016/s0022-2836(02)00221-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proline residues in the helical segments of soluble and transmembrane proteins have received special attention from both a structural and functional perspective. A feature of these helices is the structural distortion termed "proline-kink", which has been associated with the presence of the proline residue. However, a recent report on the yeast heat-shock transcription factor of Kluyveromyces lactis (HSF_KL) suggests that these proline-associated deformations can be achieved in the absence of proline residues, thus raising the question of the mechanisms responsible for the structural mimicry of proline-related features. In this study, the specific interactions responsible for the distortion were characterized by comparative analysis of the atomic details of the packing interactions that surround the evolutionarily conserved proline-kink in the alpha2 helix of HSF_KL and a set of 39 structurally related proteins that lacked the distortion. The mechanistic details inferred from this analysis were confirmed with molecular dynamics simulations. The study shows that the packing interactions between the alpha2 and alpha1 helices in HSF_KL are responsible for the stabilization of the conserved kink, whether a proline residue that divides the helix into segments is present or not. The proline-kink can facilitate the formation of tertiary packing interactions that would otherwise not be possible. However, it is the ability to establish differential packing interactions for the helix segments, rather than the structural properties of the proline-kink itself, that emerges as the key factor for the characteristic distortion.
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Affiliation(s)
- Marc A Ceruso
- Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029-6574, USA
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