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Figiel M, Łakomska J, Miłek P, Dziedzicka‐Wasylewska M, Górecki A. The transcription factor
YY
2 has less momentous properties of an intrinsically disordered protein than its paralog
YY
1. FEBS Lett 2019; 593:1787-1798. [DOI: 10.1002/1873-3468.13457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Małgorzata Figiel
- Department of Physical Biochemistry Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Julia Łakomska
- Department of Physical Biochemistry Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Piotr Miłek
- Department of Physical Biochemistry Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Marta Dziedzicka‐Wasylewska
- Department of Physical Biochemistry Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Andrzej Górecki
- Department of Physical Biochemistry Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
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2
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Górecki A, Bonarek P, Górka AK, Figiel M, Wilamowski M, Dziedzicka-Wasylewska M. Intrinsic disorder of human Yin Yang 1 protein. Proteins 2015; 83:1284-96. [PMID: 25963536 DOI: 10.1002/prot.24822] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 04/27/2015] [Accepted: 05/02/2015] [Indexed: 01/26/2023]
Abstract
YY1 (Yin Yang 1) is a zinc finger protein with an essential role in various biological functions via DNA- and protein-protein interactions with numerous partners. YY1 is involved in the regulation of a broad spectrum of cellular processes such as embryogenesis, proliferation, tumorigenesis, and snRNA transcription. The more than 100 reported targets of the YY1 protein suggest that it contains intrinsically disordered regions that are involved in such diverse interactions. Here, we present a study of the structural properties of human YY1 using several biochemical and biophysical techniques (fluorescence, circular dichroism, gel filtration chromatography, proteolytic susceptibility) together with various bioinformatics approaches. To facilitate our exploration of the YY1 structure, the full-length protein as well as an N-terminal fragment (residues 1-295) and the C-terminal DNA binding domain were used. We found the N-terminus to be a non-compact fragment of YY1 with little residual secondary structure and lacking a well-defined tertiary structure. The results of our study indicate that YY1 belongs to the family of intrinsically disordered proteins (IDPs), which exist natively in a partially unfolded conformation.
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Affiliation(s)
- Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Adam Kazimierz Górka
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Małgorzata Figiel
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Mateusz Wilamowski
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
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Zayats M, Brenner AJ, Searson PC. Protein imprinting in polyacrylamide-based gels. Biomaterials 2014; 35:8659-68. [PMID: 25034963 PMCID: PMC4352324 DOI: 10.1016/j.biomaterials.2014.05.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/28/2014] [Indexed: 11/27/2022]
Abstract
Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding.
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Affiliation(s)
- Maya Zayats
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Brenner
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Peter C Searson
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA.
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Zayats M, Kanwar M, Ostermeier M, Searson PC. Molecular Imprinting of Maltose Binding Protein: Tuning Protein Recognition at the Molecular Level. Macromolecules 2011. [DOI: 10.1021/ma200355j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maya Zayats
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Manu Kanwar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter C. Searson
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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A label-free electrochemical immunoassay for IgG detection based on the electron transfer. Talanta 2010; 83:42-7. [PMID: 21035641 DOI: 10.1016/j.talanta.2010.08.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/19/2010] [Accepted: 08/24/2010] [Indexed: 11/22/2022]
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6
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Sun S, Ma H, Chen X, Zhang N, Wu D, Du B, Wei Q. Fluorimetric determination of proteins using 4-chloro-(2′-hydroxylophenylazo)rhodanine-Ti(IV) complex as a spectral probe. LUMINESCENCE 2008; 23:333-7. [DOI: 10.1002/bio.1041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Domínguez-Vidal A, Saenz-Navajas MP, Ayora-Cañada MJ, Lendl B. Detection of Albumin Unfolding Preceding Proteolysis Using Fourier Transform Infrared Spectroscopy and Chemometric Data Analysis. Anal Chem 2006; 78:3257-64. [PMID: 16689524 DOI: 10.1021/ac0520137] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrolysis of bovine serum albumin with protease K at 60 degrees C has been studied by means of infrared spectroscopy. Two-dimensional correlation spectroscopy (2DCoS) has been used to study spectral changes in the reaction. The use of the multivariate curve resolution-alternating least-squares method applied to infrared measurements allowed the recovery of pure infrared spectra and concentration profiles of the different species involved in the reaction. Special attention was paid to the careful inspection of residuals again using 2DCoS. In this way, a heat-induced unfolding step previous to protein hydrolysis was identified. The infrared spectra of the intermediate species showed a more disordered structure than native albumin, the decrease in alpha-helix conformation being especially noticeable. The formation of beta-sheet aggregates due to heating was detected too.
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Affiliation(s)
- Ana Domínguez-Vidal
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
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