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Analysis of Heterodimeric "Mutual Synergistic Folding"-Complexes. Int J Mol Sci 2019; 20:ijms20205136. [PMID: 31623284 PMCID: PMC6829572 DOI: 10.3390/ijms20205136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.
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Kalaydzkiev H, Ivanova P, Silva CL, Chalova VI. Functional Properties of Protein Isolate and Acid Soluble Protein-Rich Ingredient Co-Produced from Ethanol-Treated Industrial Rapeseed Meal. POL J FOOD NUTR SCI 2019. [DOI: 10.31883/pjfns-2019-0007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Chen CW, Chang KP, Ho CW, Chang HP, Chu YW. KStable: A Computational Method for Predicting Protein Thermal Stability Changes by K-Star with Regular-mRMR Feature Selection. ENTROPY 2018; 20:e20120988. [PMID: 33266711 PMCID: PMC7512587 DOI: 10.3390/e20120988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/11/2018] [Accepted: 12/16/2018] [Indexed: 11/24/2022]
Abstract
Thermostability is a protein property that impacts many types of studies, including protein activity enhancement, protein structure determination, and drug development. However, most computational tools designed to predict protein thermostability require tertiary structure data as input. The few tools that are dependent only on the primary structure of a protein to predict its thermostability have one or more of the following problems: a slow execution speed, an inability to make large-scale mutation predictions, and the absence of temperature and pH as input parameters. Therefore, we developed a computational tool, named KStable, that is sequence-based, computationally rapid, and includes temperature and pH values to predict changes in the thermostability of a protein upon the introduction of a mutation at a single site. KStable was trained using basis features and minimal redundancy–maximal relevance (mRMR) features, and 58 classifiers were subsequently tested. To find the representative features, a regular-mRMR method was developed. When KStable was evaluated with an independent test set, it achieved an accuracy of 0.708.
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Affiliation(s)
- Chi-Wei Chen
- Department of Computer Science and Engineering, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Kai-Po Chang
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
- China Medical University Hospital, No. 2, Yude Rd., Taichung 404, Taiwan
| | - Cheng-Wei Ho
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Hsung-Pin Chang
- Department of Computer Science and Engineering, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Yen-Wei Chu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
- Biotechnology Center, Agricultural Biotechnology Center, Institute of Molecular Biology, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Kuo Kuang Rd., Taichung 402, Taiwan
- Correspondence: ; Tel.: +886-4-22840338 (ext. 7041)
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Magyar C, Mentes A, Fichó E, Cserző M, Simon I. Physical Background of the Disordered Nature of "Mutual Synergetic Folding" Proteins. Int J Mol Sci 2018; 19:ijms19113340. [PMID: 30373142 PMCID: PMC6274838 DOI: 10.3390/ijms19113340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined 3D structure. Their disordered nature enables them to interact with several other proteins and to fulfil their vital biological roles, in most cases after coupled folding and binding. In this paper, we analyze IDPs involved in a new mechanism, mutual synergistic folding (MSF). These proteins define a new subset of IDPs. Recently we collected information on these complexes and created the Mutual Folding Induced by Binding (MFIB) database. These protein complexes exhibit considerable structural variation, and almost half of them are homodimers, but there is a significant amount of heterodimers and various kinds of oligomers. In order to understand the basic background of the disordered character of the monomers found in MSF complexes, the simplest part of the MFIB database, the homodimers are analyzed here. We conclude that MFIB homodimeric proteins have a larger solvent-accessible main-chain surface area on the contact surface of the subunits, when compared to globular homodimeric proteins. The main driving force of the dimerization is the mutual shielding of the water-accessible backbones and the formation of extra intermolecular interactions.
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Affiliation(s)
- Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Anikó Mentes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Erzsébet Fichó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
- Department of Physiology, Faculty of Medicine, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary.
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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Jafari Azad V, Kasravi S, Alizadeh Zeinabad H, Memar Bashi Aval M, Saboury AA, Rahimi A, Falahati M. Probing the conformational changes and peroxidase-like activity of cytochrome c upon interaction with iron nanoparticles. J Biomol Struct Dyn 2016; 35:2565-2577. [PMID: 27632558 DOI: 10.1080/07391102.2016.1222972] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein, the interaction of iron nanoparticle (Fe-NP) with cytochrome c (Cyt c) was investigated, and a range of techniques such as dynamic light scattering (DLS), zeta potential measurements, static and synchronous fluorescence spectroscopy, near and far circular dichroism (CD) spectroscopy, and ultraviolet-visible (UV-vis) spectroscopy were used to analyze the interaction between Cyt c and Fe-NP. DLS and zeta potential measurements showed that the values of hydrodynamic radius and charge distribution of Fe-NP are 83.95 ± 3.7 nm and 4.5 ± .8 mV, respectively. The fluorescence spectroscopy results demonstrated that the binding of Fe-NP with Cyt c is mediated by hydrogen bonds and van der Waals interactions. Also Fe-NP induced conformational changes in Cyt c and reduced the melting temperature value of Cyt c from 79.18 to 71.33°C. CD experiments of interaction between Fe-NP and Cyt c revealed that the secondary structure of Cyt c with the dominant α-helix structures remained unchanged whereas the tertiary structure and heme position of Cyt c are subjected to remarkable changes. Absorption spectroscopy at 695 nm revealed that Fe-NP considerably disrupt the Fe…S(Met80) bond. In addition, the UV-vis experiment showed the peroxidase-like activity of Cyt c upon interaction with Fe-NP. Hence, the data indicate the Fe-NP results in unfolding of Cyt c and subsequent peroxidase-like activity of denatured species. It was concluded that a comprehensive study of the interaction of Fe-NP with biological system is a crucial step for their potential application as intracellular delivery carriers and medicinal agents.
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Affiliation(s)
- Vida Jafari Azad
- a Faculty of Advance Science and Technology, Department of Nanotechnology , Islamic Azad University (IAUPS) , Pharmaceutical Sciences Branch, Tehran , Iran
| | - Shahab Kasravi
- b Biology Department , Islamic Azad University , Tehran Medical Sciences Branch, Tehran , Iran
| | - Hojjat Alizadeh Zeinabad
- c Brain Engineering Research Center , Institute for Research in Fundamental Sciences (IPM) , P.O.Box 19395-5746, Tehran , Iran
| | - Mehri Memar Bashi Aval
- a Faculty of Advance Science and Technology, Department of Nanotechnology , Islamic Azad University (IAUPS) , Pharmaceutical Sciences Branch, Tehran , Iran
| | - Ali Akbar Saboury
- d Institute of Biochemistry and Biophysics, University of Tehran , Tehran , Iran
| | - Arash Rahimi
- e Faculty of Basic Science, Department of Biophysics , Islamic Azad University , Science and Research Branch, Tehran , Iran
| | - Mojtaba Falahati
- a Faculty of Advance Science and Technology, Department of Nanotechnology , Islamic Azad University (IAUPS) , Pharmaceutical Sciences Branch, Tehran , Iran
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