1
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Moodley D, Botes A. A carboxymethyl cellulase from the yeast Cryptococcus gattii WM276: Expression, purification and characterisation. Protein Expr Purif 2025; 225:106594. [PMID: 39197672 DOI: 10.1016/j.pep.2024.106594] [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: 05/08/2024] [Revised: 08/21/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Cryptococcus gattii and its medical implications have been extensively studied. There is, however, a significant knowledge gap regarding cryptococcal survival in its environmental niche, namely woody material, which is glaring given that infection is linked to environmental populations. A gene from C. gattii (WM276), the predominant global molecular type (VGI), has been sequenced and annotated as a putative cellulase. It is therefore, of both medical and industrial intertest to delineate the structure and function of this enzyme. A homology model of the enzyme was constructed as a fusion protein to a maltose binding protein (MBP). The CGB_E4160W gene was overexpressed as an MBP fusion enzyme in Escherichia coli T7 cells and purified to homogeneity using amylose affinity chromatography. The structural and functional character of the enzyme was investigated using fluorescence spectroscopy and enzyme activity assays, respectively. The optimal enzyme pH and temperature were found to be 6.0 and 50 °C, respectively, with an optimal salt concentration of 500 mM. Secondary structure analysis using Far-UV CD reveals that the MBP fusion protein is primarily α-helical with some β-sheets. Intrinsic tryptophan fluorescence illustrates that the MBP-cellulase undergoes a conformational change in the presence of its substrate, CMC-Na+. The thermotolerant and halotolerant nature of this particular cellulase, makes it useful for industrial applications, and adds to our understanding of the pathogen's environmental physiology.
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Affiliation(s)
- Dylan Moodley
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Botes
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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2
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Arya A, Jain A, Kishore N. Thermodynamics of modulation of interaction of α-helix inducer 2, 2, 2-trifluoroethanol with lysozyme in presence of cationic, anionic and non-ionic surfactants. J Biomol Struct Dyn 2024; 42:7289-7303. [PMID: 37493410 DOI: 10.1080/07391102.2023.2239922] [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: 04/07/2023] [Accepted: 07/17/2023] [Indexed: 07/27/2023]
Abstract
The interactions of anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB) and nonionic triton X-100 (TX-100) surfactants with lysozyme at pH = 2.4 have been studied individually as well as in combination with 2,2,2-trifluoroetanol (TFE). Urea has also been used in combination with surfactants. By using these combinations, efforts have been made to obtain partially folded conformations of the protein in the presence of surfactants and effect of α-helix inducer 2,2,2-trifluoroethanol on these intermediate states. Thermodynamic analysis of all these interactions has been done employing a combination of UV-visible, fluorescence and circular dichroism spectroscopies. The results have been correlated with each other and characterized qualitatively as well as quantitatively. At lower concentration of surfactant, the thermodynamic parameters indicated the destabilizing effect of SDS, stabilizing effect of CTAB and unappreciable destabilizing impact of TX-100 on lysozyme. The enhancement in destabilization effect or reduction in stabilization effect of surfactants on lysozyme in the presence of TFE and urea has also been indicated.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anju Arya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
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3
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Jain A, Judy E, Kishore N. Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach. J Phys Chem B 2024; 128:5344-5362. [PMID: 38773936 DOI: 10.1021/acs.jpcb.4c01751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Fagan A, Bateman LM, O’Shea JP, Crean AM. Elucidating the Degradation Pathways of Human Insulin in the Solid State. JOURNAL OF ANALYSIS AND TESTING 2024; 8:288-299. [PMID: 39184306 PMCID: PMC11338979 DOI: 10.1007/s41664-024-00302-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 08/27/2024]
Abstract
While there have been significant advances in the development of peptide oral dosage forms in recent years, highlighted by the clinical and commercial success of approved peptides such as Rybelsus®, there remain several barriers in the way of broad range applicability of this approach to peptide delivery. One such barrier includes the poor physical and chemical stability inherent to their structures, which persists in the solid state although degradation typically occurs at different rates and via different pathways in comparison to the solution state. Using insulin as a model peptide, this work sought to contribute to the development of analytical techniques for investigating common insulin degradation pathways. Chemically denatured, deamidated and aggregated samples were prepared and used to benchmark circular dichroism spectroscopy, reverse phase HPLC and size exclusion chromatography methods for the investigation of unfolding, chemical modifications and covalent aggregation of the insulin molecule respectively. Solid state degraded samples were prepared by heating insulin powder at 60 °C and 75% relative humidity for 1, 3, 5 and 7 d, and the degradation profiles of the samples were evaluated and compared with those observed in solution. While no unfolding was observed to occur, significant deamidation and covalent aggregation were detected. Reductive disulfide bond cleavage using dithiothreitol allowed for separation of the insulin A- and B-chains, offering a facile yet novel means of assessing the mechanisms of deamidation and covalent aggregation occurring in the solid state. Supplementary Information The online version contains supplementary material available at 10.1007/s41664-024-00302-5.
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Affiliation(s)
- Andrew Fagan
- SSPC, the SFI Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, Cork, T12 YT20 Ireland
| | - Lorraine M. Bateman
- School of Pharmacy, University College Cork, Cork, T12 YT20 Ireland
- Analytical and Biological Chemistry Research Facility (ABCRF), University College Cork, Cork, T12 YN60 Ireland
- School of Chemistry, University College Cork, Cork, T12 YN60 Ireland
| | - Joseph P. O’Shea
- School of Pharmacy, University College Cork, Cork, T12 YT20 Ireland
| | - Abina M. Crean
- SSPC, the SFI Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, Cork, T12 YT20 Ireland
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5
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Wang Y, Shen J, Zou B, Zhang L, Xu X, Wu C. Determination of the critical pH for unfolding water-soluble cod protein and its effect on encapsulation capacities. Food Res Int 2023; 174:113621. [PMID: 37986474 DOI: 10.1016/j.foodres.2023.113621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Hydrophobic polyphenols, with a variety of physiological activities, are often practically limited due to their low water solubility and chemical instability, among which curcumin (Cur) is a representative hydrophobic polyphenol. To improve Cur, the cod protein (CP)-Cur composite particles (CP-Cur) were successfully prepared using the pH-shift method, but this pH-shift method (7-12-7) required a higher pH, which limited application and increased cost. The critical pH of CP structure unfolding during pH-shift and its encapsulation effect on Cur were investigated in this paper. During the pH-shift process, the critical pH of the structural unfolding of CP was pH 10, and the degree of protein structure unfolding was higher, which was attributed to the increasing electrostatic repulsion, and the weakened hydrogen bond and hydrophobic interaction. The encapsulation efficiency of CP-Cur formed after pH 10-shift was higher than that formed after pH 9.8-shift, which increased by 22.17 %. At pH 9.8, the binding sites in CP reached saturation at the molar ratio of 10, while at pH 10 and 10.2, the binding sites in CP both reached saturation at the molar ratio of 14, also indicating that the protein treated with critical pH could bind more Cur. The binding between Cur and CP was mostly hydrophobic interaction, accompanied by hydrogen bonding and electrostatic interactions. The above results verified the necessity of critical pH in the experiment, indicating that critical pH could indeed improve the encapsulation effect and obtain a higher encapsulation efficiency. This work will help improve the large-scale application of hydrophobic functional substances in production.
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Affiliation(s)
- Yuying Wang
- College of Food Science, Dalian Polytechnic University, Dalian 116034, China; College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China; State Key Laboratory of Marine Food Processing and Safety Control, China; National Engineering Research Center of Seafood, China
| | - Jing Shen
- Ningjin Market Supervision Administration, Dezhou 253400, China
| | - Bowen Zou
- College of Food Science, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing and Safety Control, China; National Engineering Research Center of Seafood, China
| | - Ling Zhang
- College of Food Science, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing and Safety Control, China; National Engineering Research Center of Seafood, China
| | - Xianbing Xu
- College of Food Science, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing and Safety Control, China; National Engineering Research Center of Seafood, China
| | - Chao Wu
- College of Food Science, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing and Safety Control, China; National Engineering Research Center of Seafood, China.
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6
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Nirmalraj PN, Rossell MD, Dachraoui W, Thompson D, Mayer M. In Situ Observation of Chemically Induced Protein Denaturation at Solvated Interfaces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:48015-48026. [PMID: 37797325 PMCID: PMC10591235 DOI: 10.1021/acsami.3c10510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Proteins unfold in chaotropic salt solutions, a process that is difficult to observe at the single protein level. The work presented here demonstrates that a liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope make it possible to observe chemically induced protein unfolding. To illustrate this capability, ferritin proteins were deposited on a graphene surface, and the concentration-dependent urea- or guanidinium-induced changes of morphology were monitored for holo-ferritin with its ferrihydrite core as well as apo-ferritin without this core. Depending on the chaotropic agent the liquid-based imaging setup captured an unexpected transformation of natively folded holo-ferritin proteins into rings after urea treatment but not after guanidinium treatment. Urea treatment of apo-ferritin did not result in nanorings, confirming that nanorings are a specific signature of denaturation of holo-ferritins after exposture to sufficiently high urea concentrations. Mapping the in situ images with molecular dynamics simulations of ferritin subunits in urea solutions suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and also disrupts the water H-bonding network in the ferritin solvation shell. Our findings deepen the understanding of protein denaturation studied using label-free techniques operating at the solid-liquid interface.
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Affiliation(s)
- Peter Niraj Nirmalraj
- Transport
at Nanoscale Interfaces Laboratory, Swiss
Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Marta D. Rossell
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Walid Dachraoui
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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7
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Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofström C, Ohlin M, Walldén K, Buggert M, Hammarström L, Marcotte H, Pan-Hammarström Q, Andréll J, Syrén PO. Design, structure and plasma binding of ancestral β-CoV scaffold antigens. Nat Commun 2023; 14:6527. [PMID: 37845250 PMCID: PMC10579346 DOI: 10.1038/s41467-023-42200-x] [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: 09/01/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.
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Affiliation(s)
- David Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stelios Vlachiotis
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Persson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Camilla Hofström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Mats Ohlin
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Karin Walldén
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juni Andréll
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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8
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Jakob LA, Mesurado T, Jungbauer A, Lingg N. Increase in cysteine-mediated multimerization under attractive protein-protein interactions. Prep Biochem Biotechnol 2022; 53:891-905. [PMID: 36576211 DOI: 10.1080/10826068.2022.2158471] [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] [Indexed: 12/29/2022]
Abstract
The CASPON enzyme became an interesting enzyme for fusion protein processing because it generates an authentic N-terminus. However, the high cysteine content of the CASPON enzyme may induce aggregation via disulfide-bond formation, which can reduce enzymatic activity and be considered a critical quality attribute. Different multimerization states of the CASPON enzyme were isolated by preparative size exclusion chromatography and analyzed with respect to multimerization propensity and enzymatic activity. The impact of co-solutes on multimerization was studied in solution and in adsorbed state. Furthermore, protein-protein interactions in the presence of different co-solutes were measured by self-interaction chromatography and were then correlated to the multimerization propensity. The dimer was the most stable and active species with 50% higher enzymatic activity than the tetramer. Multimerization was mainly governed by a cysteine-mediated pathway, as indicated by DTT-induced reduction of most caspase multimers. In the presence of ammonium sulfate, attractive protein-protein interactions were consistent with those observed for higher multimerization when the cysteine-mediated pathway was followed. Multimerization was also observed under attractive conditions on a chromatographic stationary phase. These findings corroborate common rules to perform protein purification with low residence time to avoid disulfide bond formation and conformational change of the protein upon adsorption.
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Affiliation(s)
- Leo A Jakob
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tomás Mesurado
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Nico Lingg
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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9
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Takita T, Sakuma H, Ohashi R, Nilouyal S, Nemoto S, Wada M, Yogo Y, Yasuda K, Ikushiro S, Sakaki T, Yasukawa K. Comparison of the stability of CYP105A1 and its variants engineered for production of active forms of vitamin D. Biosci Biotechnol Biochem 2022; 86:444-454. [PMID: 35134837 DOI: 10.1093/bbb/zbac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/21/2022] [Indexed: 11/14/2022]
Abstract
CYP105A1 from Streptomyces griseolus converts vitamin D3 to its biologically active form, 1α,25-dihydroxy vitamin D3. R73A/R84A mutation enhanced the 1α- and 25-hydroxylation activity for vitamin D3, while M239A mutation generated the 1α-hydroxylation activity for vitamin D2. In this study, the stability of six CYP105A1 enzymes, including 5 variants (R73A/R84A, M239A, R73A/R84A/M239A (=TriA), TriA/E90A, and TriA/E90D), was examined. Circular dichroism analysis revealed that M239A markedly reduces the enzyme stability. Protein fluorescence analysis disclosed that these mutations, especially M239A, induce large changes in the local conformation around Trp residues. Strong stabilizing effect of glycerol was observed. Nondenaturing PAGE analysis showed that CYP105A1 enzymes are prone to self-association. Fluorescence analysis using a hydrophobic probe 8-anilino-1-naphthalenesulfonic acid suggested that M239A mutation enhances self-association and that E90A and E90D mutations, in cooperation with M239A, accelerate self-association with little effect on the stability.
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Affiliation(s)
- Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiro Sakuma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ren Ohashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Somaye Nilouyal
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sho Nemoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Moeka Wada
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuya Yogo
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Kaori Yasuda
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan.,Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Toshiyuki Sakaki
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan.,Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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10
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Towards a generic prototyping approach for therapeutically-relevant peptides and proteins in a cell-free translation system. Nat Commun 2022; 13:260. [PMID: 35017494 PMCID: PMC8752827 DOI: 10.1038/s41467-021-27854-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Advances in peptide and protein therapeutics increased the need for rapid and cost-effective polypeptide prototyping. While in vitro translation systems are well suited for fast and multiplexed polypeptide prototyping, they suffer from misfolding, aggregation and disulfide-bond scrambling of the translated products. Here we propose that efficient folding of in vitro produced disulfide-rich peptides and proteins can be achieved if performed in an aggregation-free and thermodynamically controlled folding environment. To this end, we modify an E. coli-based in vitro translation system to allow co-translational capture of translated products by affinity matrix. This process reduces protein aggregation and enables productive oxidative folding and recycling of misfolded states under thermodynamic control. In this study we show that the developed approach is likely to be generally applicable for prototyping of a wide variety of disulfide-constrained peptides, macrocyclic peptides with non-native bonds and antibody fragments in amounts sufficient for interaction analysis and biological activity assessment. Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.
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11
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Das N, Yadav S, Negi KS, Tariff E, Sen P. Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain: A Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder. BBA ADVANCES 2022; 2:100041. [PMID: 37082607 PMCID: PMC10074955 DOI: 10.1016/j.bbadva.2022.100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022] Open
Abstract
Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. However, it is not easy to directly correlate an enzyme's dynamics and activity due to biosystems' enormous complexity. amongst many factors, structure and dynamics are two prime aspects that combinedly control the activity. Therefore, having a direct correlation between protein dynamics and activity is not straightforward. Herein, we observed and correlated the structural, functional, and dynamical responses of an industrially crucial proteolytic enzyme, bromelain with three versatile classes of chemicals: GnHCl (protein denaturant), sucrose (protein stabilizer), and Ficoll-70 (macromolecular crowder). The only free cysteine (Cys-25 at the active-site) of bromelain has been tagged with a cysteine-specific dye to unveil the structural and dynamical changes through various spectroscopic studies both at bulk and at the single molecular level. Proteolytic activity is carried out using casein as the substrate. GnHCl and sucrose shows remarkable structure-dynamics-activity relationships. Interestingly, with Ficoll-70, structure and activity are not correlated. However, microsecond dynamics and activity are beautifully correlated in this case also. Overall, our result demonstrates that bromelain dynamics in the microsecond timescale around the active-site is probably a key factor in controlling its proteolytic activity.
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12
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Stepwise oxidations play key roles in the structural and functional regulations of DJ-1. Biochem J 2021; 478:3505-3525. [PMID: 34515295 DOI: 10.1042/bcj20210245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and functional changes of DJ-1 in response to oxidative stress. Human DJ-1 has three cysteine residues (Cys46, Cys53 and Cys106). We found that, in addition to Cys106, Cys46 is the most reactive cysteine residue in DJ-1, which was identified employing an NPSB-B chemical probe (Ctag) that selectively reacts with redox-sensitive cysteine sulfhydryl. Peroxidatic Cys46 readily formed an intra-disulfide bond with adjacent resolving Cys53, which was identified with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS) employing DBond algorithm under the non-reducing condition. Mutants (C46A and C53A), not forming Cys46-Cys53 disulfide cross-linking, increased oxidation of Cys106 to sulfinic and sulfonic acids. Furthermore, we found that DJ-1 C46A mutant has distorted unstable structure identified by biochemical assay and employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS) analysis. All three Cys mutants lost antioxidant activities in SN4741 cell, a dopaminergic neuronal cell, unlike WT DJ-1. These findings suggest that all three Cys residues including Cys46-Cys53 disulfide cross-linking are required for maintaining the structural integrity, the regulation process and cellular function as an antioxidant protein. These studies broaden the understanding of regulatory mechanisms of DJ-1 that operate under oxidative conditions.
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Thakur M, Sharma N, Rai AK, Singh SP. A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch. BIORESOURCE TECHNOLOGY 2021; 320:124288. [PMID: 33120064 DOI: 10.1016/j.biortech.2020.124288] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Pullulanase is a potent enzyme for starch debranching. In this study, a novel type I pullulanase (PulM) was identified from the metagenome of a thermal aquatic habitat that exhibits optimal activity of debranching at 40 °C temperature and pH 6.0 to 7.0. More than 50% enzymatic activity was detected at the low temperature of 4 °C, determining it a cold-active type I pullulanase. It was able to efficiently catalyze the hydrolysis of α-1,6-glycosidic linkages in pullulan, with a specific activity of 177 U mg-1. The results determined PulM to be a potential starch debranching biocatalyst, causing a significant increase of about 80% in the apparent amylose content of potato starch. Retrogradation of the debranched starch resulted in the formation of resistant starch 3. The yield of resistant starch was estimated to be about 45%. The resistant starch exhibited higher crystallinity, enhanced heat-stability, and resistance to α-amylase digestion, as compared to native starch.
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Affiliation(s)
- Monika Thakur
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Sector 81, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Sector 81, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Sikkim Centre, Tadong, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Sector 81, Mohali, India.
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14
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Khan MA, Akram MF, Alam K, Ahsan H, Rizvi MA. Peroxynitrite-Mediated Structural Changes in Histone H2A: Biochemical and Biophysical Analysis. Protein Pept Lett 2020; 27:989-998. [DOI: 10.2174/0929866527666200427213722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 11/22/2022]
Abstract
Background:
Peroxynitrite, a nitrating and oxidizing agent, is formed by the interaction
between nitric oxide and superoxide radicals. H2A histone is a basic nucleoprotein and is one of
the major core histones responsible for packaging DNA. It has been shown that they are highly sensitive
to oxidizing and nitrating agents.
Objective:
Nitration of tyrosine residues in proteins by peroxynitrite is regarded as a marker of
nitrosative damage. The dityrosine bond, an oxidative covalent cross-link between two tyrosines in
protein, is increasingly identified as a marker of oxidative stress, aging and neurodegerative
diseases.
Methods:
Peroxinitrite-mediated nitration and dinitration in H2A histone was assessed by various
biophysical techniques.
Results:
The data presented in this study showed that the dityrosine content was found to be elevated
in H2A histone modified with peroxynitrite. The formation of dityrosine showed a decrease in
fluorescence intensity, generation of a new peak in FT-IR, increase in hydrodynamic size, and loss
of secondary and tertiary structure of H2A resulting in a partially folded structure.
Conclusion:
We report that H2A may undergo conformational and structural changes under nitrosative
and oxidative stress from the deleterious effects of peroxynitrite.
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Affiliation(s)
- Md. Asad Khan
- Faculty of Dentistry, Jamia Millia Islamia, New Delhi-110025, India
| | - Md. Faiz Akram
- Faculty of Dentistry, Jamia Millia Islamia, New Delhi-110025, India
| | - Khursheed Alam
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh-202002, India
| | - Haseeb Ahsan
- Faculty of Dentistry, Jamia Millia Islamia, New Delhi-110025, India
| | - Moshahid A. Rizvi
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
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Cataract-Associated New Mutants S175G/H181Q of βΒ2-Crystallin and P24S/S31G of γD-Crystallin Are Involved in Protein Aggregation by Structural Changes. Int J Mol Sci 2020; 21:ijms21186504. [PMID: 32899552 PMCID: PMC7555777 DOI: 10.3390/ijms21186504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022] Open
Abstract
β/γ-Crystallins, the main structural protein in human lenses, have highly stable structure for keeping the lens transparent. Their mutations have been linked to cataracts. In this study, we identified 10 new mutations of β/γ-crystallins in lens proteomic dataset of cataract patients using bioinformatics tools. Of these, two double mutants, S175G/H181Q of βΒ2-crystallin and P24S/S31G of γD-crystallin, were found mutations occurred in the largest loop linking the distant β-sheets in the Greek key motif. We selected these double mutants for identifying the properties of these mutations, employing biochemical assay, the identification of protein modifications with nanoUPLC-ESI-TOF tandem MS and examining their structural dynamics with hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that both double mutations decrease protein stability and induce the aggregation of β/γ-crystallin, possibly causing cataracts. This finding suggests that both the double mutants can serve as biomarkers of cataracts.
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16
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Mirdha L, Chakraborty H. Fluorescence quenching by ionic liquid as a potent tool to study protein unfolding intermediates. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113408] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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17
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Rajan P, Mishra PKK, Joshi P. Defining the complement C3 binding site and the antigenic region of Haemonchus contortus GAPDH. Parasite Immunol 2019; 41:e12611. [PMID: 30548600 DOI: 10.1111/pim.12611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/12/2018] [Accepted: 12/04/2018] [Indexed: 11/28/2022]
Abstract
Haemonchus contortus is an economically important parasite that survives the host defense system by modulating the immune response. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is secreted by the parasite and the host responds by producing anti-enzyme antibodies. The enzyme inhibits complement cascade, an arm of the innate immunity, by binding to complement C3. In this study, the C3 binding site and the antigenic region of the enzyme were identified by generating short recombinant fragments and deleting a defined region of the enzyme. Using these proteins in ligand overlay and plate binding assay, the C3 binding region of GAPDH was localized within the 38 residues represented by 77-114 amino acids whereas one of the antigenic regions was identified in between 77 and 171 amino acids. In addition, deletion of amino acids 77 to 171 from GAPDH (fragment AB) also showed weak immunogenicity but lacked C3 binding activity. Fragment D comprising 95 residues (77-171), had both the C3 binding activity as well as immunogenicity like the parent enzyme, also stimulated host peripheral blood mononuclear cells in vitro. This truncated GAPDH moiety was stable at refrigerated temperature for at least 12 weeks and appears as a promising new therapeutic tool considering its longer shelf life as compared to the parent protein.
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Affiliation(s)
- Parvathy Rajan
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Prasanta K K Mishra
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Paritosh Joshi
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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18
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Sekhon G, Singh R. Human aldose reductase unfolds through an intermediate. F1000Res 2019; 8:564. [PMID: 31723418 PMCID: PMC6844136 DOI: 10.12688/f1000research.18963.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Human aldose reductase (hAR) is the first and rate-limiting enzyme of the polyol pathway. For the development of secondary complications of diabetes in chronic hyperglycemic conditions, one of the critical factors is the increased flux of glucose through the polyol pathway. Due to this clinical implication, hAR attracted considerable attention from the drug discovery perspective. In spite of extensive characterization in the context of biochemical and structural aspects, we know very little about the unfolding behavior of hAR. This study reports equilibrium unfolding studies of hAR. Methods: We carried out thermal denaturation and chemical-induced equilibrium unfolding studies of hAR monitored by circular dichroism and fluorescence spectroscopy. Results: Thermal denaturation studies presented a classical picture of two-state unfolding from native to the denatured state. The data was used to derive thermodynamic parameters and study the thermostability of hAR. Chemical induced equilibrium unfolding studies led us to discover an intermediate state, which gets populated at 3.5-4.0 M and 0.7-2.0 M of urea and GuHCl, respectively. Thermodynamic parameters derived from chemical-induced unfolding are in agreement with those obtained from thermal denaturation of hAR. Conclusion: This study revealed that aldose reductase unfolds from native to the unfolded state via an intermediate. Assessment of the thermodynamic stability of native, intermediate, and unfolded states shows that significant energy barriers separate these states, which ensures the cooperativity of unfolding. As hAR functions in cells that are under osmotic and oxidative stress, these
in vitro findings may have implications for its native conformation under the physiological state.
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Affiliation(s)
- Gurprit Sekhon
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| | - Ranvir Singh
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
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19
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Narang P, Yadav N, Venkatesu P. Scrutinizing the effect of various nitrogen containing additives on the micellization behavior of a triblock copolymer. J Colloid Interface Sci 2019; 553:655-665. [DOI: 10.1016/j.jcis.2019.06.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/29/2022]
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20
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Judy E, Kishore N. A look back at the molten globule state of proteins: thermodynamic aspects. Biophys Rev 2019; 11:365-375. [PMID: 31055760 PMCID: PMC6557940 DOI: 10.1007/s12551-019-00527-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/22/2019] [Indexed: 12/23/2022] Open
Abstract
Interest in protein folding intermediates lies in their significance to protein folding pathways. The molten globule (MG) state is one such intermediate lying on the kinetic (and sometimes thermodynamic) pathway between native and unfolded states. Development of our qualitative and quantitative understanding of the MG state can provide deeper insight into the folding pathways and hence potentially facilitate solution of the protein folding problem. An extensive look at literature suggests that most studies into protein MG states have been largely qualitative. Attempts to obtain quantitative insights into MG states have involved application of high-sensitivity calorimetry (differential scanning calorimetry and isothermal titration calorimetry). This review addresses the progress made in this direction by discussing the knowledge gained to date, along with the future promise of calorimetry, in providing quantitative information on the structural features of MG states. Particular attention is paid to the question of whether such states share common structural features or not. The difference in the nature of the transition from the MG state to the unfolded state, in terms of cooperativity, has also been addressed and discussed.
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Affiliation(s)
- Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
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21
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Ota C, Takano K. Spectroscopic Analysis of Protein-Crowded Environments Using the Charge-Transfer Fluorescence Probe 8-Anilino-1-Naphthalenesulfonic Acid. Chemphyschem 2019; 20:1456-1466. [PMID: 30945450 DOI: 10.1002/cphc.201900226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/01/2019] [Indexed: 12/11/2022]
Abstract
The molecular behaviors of proteins under crowding conditions are crucial for understanding the protein actions in intracellular environments. Under a crowded environment, the distance between protein molecules is almost the same size as the molecular level, thus, both the excluded volume effect and short ranged soft chemical interaction on protein surface could induce the complicated influence on the protein behavior cooperatively. Recently, various kinds of analytical approaches from macroscopic to microscopic aspects have been made to evaluate the crowding effect. The method, however, has not been established to evaluate the surface specific interactions on protein surface. In this study, the analytical method to evaluate the crowding effect has been suggested by using a charge-transfer fluorescence probe, ANS. By employing the unique property of ANS attaching to charged residues on the surface of lysozyme, the crowding effect was focused, while the case was compared as a reference, in which ANS is confined in hydrophobic pockets of BSA. Consequently, the surface specific changes of fluorescence spectra were readily observed under the crowded environment, whereas the fluorescence spectra of ANS in protein inside did not change. This result suggests the fluorescence spectra of ANS binding to protein surface have the capability to estimate the crowding effect of proteins.
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Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
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22
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Furkan M, Siddiqi MK, Zakariya SM, Khan FI, Hassan MI, Khan RH. An In Vitro elucidation of the antiaggregatory potential of Diosminover thermally induced unfolding of hen egg white lysozyme; A preventive quest for lysozyme amyloidosis. Int J Biol Macromol 2019; 129:1015-1023. [DOI: 10.1016/j.ijbiomac.2019.02.107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 01/24/2023]
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23
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Ghosh S, Salama F, Dines M, Lahav A, Adir N. Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:442-452. [PMID: 30711645 DOI: 10.1016/j.bbapap.2018.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. HspA has been shown to be important for the protection of Photosystem II and the Phycobilisome antenna complex at elevated temperatures. Heterologously expressed HspA requires the presence of 1-2 M urea to maintain its solubility at concentrations required for most characterization methods. Spectroscopic studies reveal the presence of the β-sheet structure and intactness of the tertiary fold in HspA. In vitro assays show that the HspA maintains chaperone-like activity in protecting soluble proteins from thermal aggregation. Chromatography and electron microscopy show that the HspA exists as a mixture of oligomeric forms in the presence of 2 M urea. HspA was successfully crystallized only in the presence of 2 M urea. The crystal structure of HspA shows urea-induced loss of about 30% of the secondary structure without major alteration in the tertiary structure of the protein. The electron density maps reveal changes in the hydrogen bonding network which we attribute to the presence of urea. The crystal structure of HspA demonstrates a mixture of both direct interactions between urea and protein functionalities and interactions between urea and the surrounding solvent that indirectly affect the protein, which are in accordance with previously published studies.
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Affiliation(s)
- Sudeshna Ghosh
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Faris Salama
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Monica Dines
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Avital Lahav
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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24
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Fuller AA, Huber J, Jimenez CJ, Dowell KM, Hough S, Ortega A, McComas KN, Kunkel J, Asuri P. Solution effects on the self‐association of a water‐soluble peptoid. Biopolymers 2018; 110:e23248. [DOI: 10.1002/bip.23248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Jonathan Huber
- Department of Bioengineering Santa Clara University Santa Clara California USA
| | - Christian J. Jimenez
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Kalli M. Dowell
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Samuel Hough
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Alberto Ortega
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Kyra N. McComas
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Jeffrey Kunkel
- Department of Bioengineering Santa Clara University Santa Clara California USA
| | - Prashanth Asuri
- Department of Bioengineering Santa Clara University Santa Clara California USA
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25
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Wang TF, Chi MC, Lai KL, Lin MG, Chen YY, Lo HF, Lin LL. High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue. PeerJ 2018; 6:e5863. [PMID: 30402354 PMCID: PMC6215446 DOI: 10.7717/peerj.5863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
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Affiliation(s)
- Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Kuan-Ling Lai
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan.,Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
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26
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The Pathways of the iRFP713 Unfolding Induced by Different Denaturants. Int J Mol Sci 2018; 19:ijms19092776. [PMID: 30223568 PMCID: PMC6163377 DOI: 10.3390/ijms19092776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) based on the complexes of bacterial phytochromes with their natural biliverdin chromophore are widely used as genetically encoded optical probes for visualization of cellular processes and deep-tissue imaging of cells and organs in living animals. In this work, we show that the steady-state and kinetic dependencies of the various spectral characteristics of iRFP713, developed from the bacterial phytochrome RpBphP2 and recorded at protein unfolding induced by guanidine hydrochloride (GdnHCl), guanidine thiocyanate (GTC), and urea, differ substantially. A study of the unfolding of three single-tryptophan mutant forms of iRFP713 expectedly revealed that protein unfolding begins with the dissociation of the native dimer, while the monomers remain compact. A further increase in the denaturant concentration leads to the formation of an intermediate state of iRFP713 having hydrophobic areas exposed on the protein surface (I). The total surface charge of iRFP713 (pI 5.86) changes from negative to positive with an increase in the concentration of GdnHCl and GTC because the negative charge of glutamic and aspartic acids is neutralized by forming salt bridges between the carboxyl groups and GdnH+ ions and because the guanidinium cations bind to amide groups of glutamines and asparagines. The coincidence of both the concentration of the denaturants at which the intermediate state of iRFP713 accumulates and the concentration of GdnH+ ions at which the neutralization of the surface charge of the protein in this state is ensured results in strong protein aggregation. This is evidently realized by iRFP713 unfolding by GTC. At the unfolding of the protein by GdnHCl, an intermediate state is populated at higher denaturant concentrations and a strong aggregation is not observed. As expected, protein aggregates are not formed in the presence of the urea. The aggregation of the protein upon neutralization of the charge on the macromolecule surface is the main indicator of the intermediate state of protein. The unfolded state of iRFP713, whose formation is accompanied by a significant decrease in the parameter A, was found to have a different residual structure in the denaturants used.
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27
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Thermal unfolding of human lysozyme induces aggregation: Recognition of the aggregates by antisera against the native protein. Int J Biol Macromol 2018; 113:976-982. [DOI: 10.1016/j.ijbiomac.2018.02.095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
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28
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Syed SB, Khan FI, Khan SH, Srivastava S, Hasan GM, Lobb KA, Islam A, Hassan MI, Ahmad F. Unravelling the unfolding mechanism of human integrin linked kinase by GdmCl-induced denaturation. Int J Biol Macromol 2018; 117:1252-1263. [PMID: 29885398 DOI: 10.1016/j.ijbiomac.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Integrin-linked kinase (ILK) is a ubiquitously expressed Ser/Thr kinase which plays significant role in the cell-matrix interactions and growth factor signalling. In this study, guanidinium chloride (GdmCl)-induced unfolding of kinase domain of ILK (ILK193-446) was carried out at pH 7.5 and 25 °C. Eventually, denaturation curves of mean residue ellipticity at 222 nm ([θ]222) and fluorescence emission spectrum were analysed to estimate stability parameters. The optical properties maximum emission (λmax) and difference absorption coefficient at 292 nm (Δε292) were analysed. The denaturation curve was measured only in the GdmCl molar concentration ranging 3.0-4.2 M because protein was aggregating below 3.0 M of GdmCl concentrations. The denaturation process of ILK193-446 was found as reversible at [GdmCl] ≥ 3.0 M. Moreover, a coincidence of normalized denaturation curves of optical properties ([θ]222, Δε292 and λmax) suggesting that GdmCl-induced denaturation of ILK193-446 is a two-state process. In addition, 100 ns molecular dynamics simulations were performed to see the effects of GdmCl on the structure and stability of ILK193-446. Both the spectroscopic and molecular dynamics approaches provided clear insights into the stability and conformational properties of ILK193-446.
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Affiliation(s)
- Sunayana Begum Syed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Sabab Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Saurabha Srivastava
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Kevin A Lobb
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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29
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Denaturation and Aggregation of Interferon-τ in Aqueous Solution. Pharm Res 2018; 35:137. [DOI: 10.1007/s11095-018-2418-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/22/2018] [Indexed: 10/16/2022]
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30
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Insight into the functional and structural transition of garlic phytocystatin induced by urea and guanidine hydrochloride: A comparative biophysical study. Int J Biol Macromol 2018; 106:20-29. [DOI: 10.1016/j.ijbiomac.2017.07.172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/20/2017] [Accepted: 07/29/2017] [Indexed: 01/29/2023]
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31
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Wei Y, Wahome N, Kumar P, Whitaker N, Picking WL, Middaugh CR. Effect of Phosphate Ion on the Structure of Lumazine Synthase, an Antigen Presentation System From Bacillus anthracis. J Pharm Sci 2017; 107:814-823. [PMID: 29045884 DOI: 10.1016/j.xphs.2017.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Lumazine synthase (LS) is an oligomeric enzyme involved in the biosynthesis of riboflavin in microorganisms, fungi, and plants. LS has become of significant interest to biomedical science because of its critical biological role and attractive structural properties for antigen presentation in vaccines. LS derived from Bacillus anthracis (BaLS) consists of 60 identical subunits forming an icosahedron. Its crystal structure has been solved, but its dynamic conformational properties have not yet been studied. We investigated the conformation of BaLS in response to different stress conditions (e.g., chemical denaturants, pH, and temperature) using a variety of biophysical techniques. The physical basis for these thermal transitions was studied, indicating that a molten globular state was present during chemical unfolding by guanidine HCl. In addition, BaLS showed 2 distinct thermal transitions in phosphate-containing buffers. The first transition was due to the dissociation of phosphate ions from BaLS and the second one came from the dissociation and conformational alteration of its icosahedral structure. A small conformational alteration was induced by the binding/dissociation of phosphate ions to BaLS. This work provides a closer view of the conformational behavior of BaLS and provides important information for the formulation of vaccines which use this protein.
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Affiliation(s)
- Yangjie Wei
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Newton Wahome
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Prashant Kumar
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Neal Whitaker
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - C Russell Middaugh
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047; Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047.
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32
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Fonin AV, Golikova AD, Zvereva IA, D'Auria S, Staiano M, Uversky VN, Kuznetsova IM, Turoverov KK. Osmolyte-Like Stabilizing Effects of Low GdnHCl Concentrations on d-Glucose/d-Galactose-Binding Protein. Int J Mol Sci 2017; 18:E2008. [PMID: 28925982 PMCID: PMC5618657 DOI: 10.3390/ijms18092008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 11/16/2022] Open
Abstract
The ability of d-glucose/d-galactose-binding protein (GGBP) to reversibly interact with its ligands, glucose and galactose, makes this protein an attractive candidate for sensing elements of glucose biosensors. This potential is largely responsible for attracting researchers to study the conformational properties of this protein. Previously, we showed that an increase in the fluorescence intensity of the fluorescent dye 6-bromoacetyl-2-dimetylaminonaphtalene (BADAN) is linked to the holo-form of the GGBP/H152C mutant in solutions containing sub-denaturing concentrations of guanidine hydrochloride (GdnHCl). It was hypothesized that low GdnHCl concentrations might lead to compaction of the protein, thereby facilitating ligand binding. In this work, we utilize BADAN fluorescence spectroscopy, intrinsic protein UV fluorescence spectroscopy, and isothermal titration calorimetry (ITC) to show that the sub-denaturing GdnHCl concentrations possess osmolyte-like stabilizing effects on the structural dynamics, conformational stability, and functional activity of GGBP/H152C and the wild type of this protein (wtGGBP). Our data are consistent with the model where low GdnHCl concentrations promote a shift in the dynamic distribution of the protein molecules toward a conformational ensemble enriched in molecules with a tighter structure and a more closed conformation. This promotes the increase in the configurational complementarity between the protein and glucose molecules that leads to the increase in glucose affinity in both GGBP/H152C and wtGGBP.
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Affiliation(s)
- Alexander V Fonin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
| | - Alexandra D Golikova
- Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Irina A Zvereva
- Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Sabato D'Auria
- CNR, Institute of Food Science, via Roma 64, 83100 Avellino, Italy.
| | - Maria Staiano
- CNR, Institute of Food Science, via Roma 64, 83100 Avellino, Italy.
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA.
| | - Irina M Kuznetsova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
- Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya av. 29, 195251 St. Petersburg, Russia.
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33
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Wu QY, Wei F, Zhu YY, Tong YX, Cao J, Zhou P, Li ZY, Zeng LY, Li F, Wang XY, Xu KL. Roles of amino acid residues H66 and D326 in the creatine kinase activity and structural stability. Int J Biol Macromol 2017; 107:512-520. [PMID: 28916380 DOI: 10.1016/j.ijbiomac.2017.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 11/24/2022]
Abstract
Creatine kinase (CK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphocreatine to ADP in vertebrates. CK contains a pair of highly conserved amino acids (H66 and D326) which might play an important role in sustaining the compact structure of CK by linking its N- and C- terminal domains; however the mechanism is still unclear. In this study, spectroscopic, structural modeling and protein folding experiments suggested that D326A, H66P and H66P/D326A mutations led to disruption of the hydrogen bond between those two amino acid residues and form the partially unfolded state which made it easier to be inactivated and unfolded under environmental stresses, and more prone to form insoluble aggregates. The formation of insoluble aggregates would decrease levels of active CKs which may provide clues in CK deficiency disease. Moreover, these results indicated that the degree of synergism had closely relationship to the conformational changes of CK. Thus, our results provided clues for understanding the mechanism of amino acid residues outside the active site in regulating substrate synergism.
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Affiliation(s)
- Qing-Yun Wu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Fang Wei
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuan-Yuan Zhu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Xue Tong
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiang Cao
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ping Zhou
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhen-Yu Li
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ling-Yu Zeng
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Li
- Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Xiao-Yun Wang
- College of Life Sciences, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Kai-Lin Xu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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Furkan M, Alam MT, Rizvi A, Khan K, Ali A, Naeem A. Aloe emodin, an anthroquinone from Aloe vera acts as an anti aggregatory agent to the thermally aggregated hemoglobin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 179:188-193. [PMID: 28242448 DOI: 10.1016/j.saa.2017.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 02/04/2017] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
Aggregation of proteins is a physiological process which contributes to the pathophysiology of several maladies including diabetes mellitus, Huntington's and Alzheimer's disease. In this study we have reported that aloe emodin (AE), an anthroquinone, which is one of the active components of the Aloe vera plant, acts as an inhibitor of hemoglobin (Hb) aggregation. Hb was thermally aggregated at 60°C for four days as evident by increased thioflavin T and ANS fluorescence, shifted congo red absorbance, appearance of β sheet structure, increase in turbidity and presence of oligomeric aggregates. Increasing concentration of AE partially reverses the aggregation of the model heme protein (hemoglobin). The maximum effect of AE was observed at 100μM followed by saturation at 125μM. The results were confirmed by UV-visible spectrometry, intrinsic fluorescence, ThT, ANS, congo red assay as well as transmission electron microscopy (TEM). These results were also supported by fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) which shows the disappearance of β sheet structure and appearance of α helices. This study will serve as baseline for translatory research and the development of AE based therapeutics for diseases attributed to protein aggregation.
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Affiliation(s)
- Mohammad Furkan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Md Tauqir Alam
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Asim Rizvi
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Kashan Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Abad Ali
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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35
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Bezsudnova EY, Petrova TE, Popinako AV, Antonov MY, Stekhanova TN, Popov VO. Intramolecular hydrogen bonding in the polyextremophilic short-chain dehydrogenase from the archaeon Thermococcus sibiricus and its close structural homologs. Biochimie 2015; 118:82-9. [PMID: 26300061 DOI: 10.1016/j.biochi.2015.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/19/2015] [Indexed: 01/27/2023]
Abstract
The short-chain alcohol dehydrogenase from the archaeon Thermococcus sibiricus (TsAdh319) exhibits adaptation to different kinds of stress: high temperature, high salinity, and the presence of organic solvents and denaturants. Previously a comparison of TsAdh319 with close structural homologs revealed an abnormally large number of charged residues on the surface of TsAdh319 tetramer. We further focused on the analysis of hydrogen bonding of TsAdh319 and its structural homologs from thermophilic and mesophilic organisms as a structural factor of adaptation to extreme environment. The calculation and analysis of the dynamics of hydrogen bonds of different kind were performed. In particular, the intramolecular hydrogen bonds of different kind according to their location and the type of a.a. residues involved in the bond were analyzed. TsAdh319 showed the greatest contribution of charged residues to the formation of surface hydrogen bonds, inner hydrogen bonding, and the bonds between different subunits compared to its structural homologs. Molecular dynamics simulations revealed that, of three enzyme molecules analyzed, TsAdh319 shows the least change in the number of hydrogen bonds of different kinds upon a temperature shift from 27 to 85 °C. The greatest changes were observed for a homologous enzyme from a mesophilic host. Only guanidine hydrochloride being a charged agent was able to deactivate TsAdh319. We suggest that the percentage of charged residues plays a key role in the resistance of TsAdh319 to environmental stress. The analysis shows that salt bridges in TsAdh319 serve as a universal instrument of stabilization under different extreme conditions.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation.
| | - Tatiana E Petrova
- Institute of Mathematical Problems of Biology, RAS, Institutskaya str. 4, Pushchino, 142290, Russian Federation
| | - Anna V Popinako
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation
| | - Mikhail Yu Antonov
- M.K. Ammosov North-Eastern Federal University, Belinskiy str., 58, Suite 312, Yakutsk, 677980, Republic of Sakha (Yakutia), Russian Federation
| | - Tatiana N Stekhanova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation; Dep. "Protein Factory", NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr., 1, Moscow, 123182, Russian Federation
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36
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Xi YB, Chen XJ, Zhao WJ, Yan YB. Congenital Cataract-Causing Mutation G129C in γC-Crystallin Promotes the Accumulation of Two Distinct Unfolding Intermediates That Form Highly Toxic Aggregates. J Mol Biol 2015; 427:2765-81. [DOI: 10.1016/j.jmb.2015.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/18/2015] [Accepted: 07/01/2015] [Indexed: 10/23/2022]
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37
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Barros AE, Carvalho FA, Alves FR, Carvalho JW, Tabak M. Denaturant effects on HbGp hemoglobin as monitored by 8-anilino-1-naphtalene-sulfonic acid (ANS) probe. Int J Biol Macromol 2015; 74:327-36. [DOI: 10.1016/j.ijbiomac.2014.12.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
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38
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Patra M, Mukhopadhyay C, Chakrabarti A. Probing conformational stability and dynamics of erythroid and nonerythroid spectrin: effects of urea and guanidine hydrochloride. PLoS One 2015; 10:e0116991. [PMID: 25617632 PMCID: PMC4305312 DOI: 10.1371/journal.pone.0116991] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/18/2014] [Indexed: 11/19/2022] Open
Abstract
We have studied the conformational stability of the two homologous membrane skeletal proteins, the erythroid and non-erythroid spectrins, in their dimeric and tetrameric forms respectively during unfolding in the presence of urea and guanidine hydrochloride (GuHCl). Fluorescence and circular dichroism (CD) spectroscopy have been used to study the changes of intrinsic tryptophan fluorescence, anisotropy, far UV-CD and extrinsic fluorescence of bound 1-anilinonapthalene-8-sulfonic acid (ANS). Chemical unfolding of both proteins were reversible and could be described as a two state transition. The folded erythroid spectrin and non-erythroid spectrin were directly converted to unfolded monomer without formation of any intermediate. Fluorescence quenching, anisotropy, ANS binding and dynamic light scattering data suggest that in presence of low concentrations of the denaturants (up-to 1M) hydrogen bonding network and van der Waals interaction play a role inducing changes in quaternary as well as tertiary structures without complete dissociation of the subunits. This is the first report of two large worm like, multi-domain proteins obeying twofold rule which is commonly found in small globular proteins. The free energy of stabilization (ΔGuH20) for the dimeric spectrin has been 20 kcal/mol lesser than the tetrameric from.
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Affiliation(s)
- Malay Patra
- Chemistry Department, University of Calcutta, Kolkata, West Bengal, India
| | | | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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39
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Akram M, Bhat IA, Bhat WF. Conformational alterations induced by novel green 16-E2-16 gemini surfactant in xanthine oxidase: Biophysical insights from tensiometry, spectroscopy, microscopy and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:440-50. [PMID: 26057098 DOI: 10.1016/j.saa.2015.05.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 05/07/2023]
Abstract
Herein we report the interaction of a biodegradable gemini surfactant, ethane-1,2-diyl bis(N,N-dimethyl-N-hexadecylammoniumacetoxy) dichloride (16-E2-16) with bovine milk xanthine oxidase (XO), employing tensiometry, fluorescence spectroscopy, UV spectroscopy, far-UV circular dichroism spectroscopy (CD), Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and computational molecular modeling. Surface tension results depict substantial changes in the micellar as well as interfacial parameters (CMC, ΠCMC, γCMC, Γmax, Amin, ΔGmic° and ΔGads°) of 16-E2-16 gemini surfactant upon XO combination, deciphering the interaction of XO with the gemini surfactant. Fluorescence measurements reveal that 16-E2-16 gemini surfactant causes quenching in the xanthine oxidase (XO) fluorescence spectra via static procedure and the values of various evaluated binding parameters (KSV, Kb, kq, ΔGb° and n) describe that 16-E2-16 effectively binds to XO. Three dimensional fluorescence, 8-anilino-1-naphthalene sulfonic acid (ANS) binding, F1F3 ratio, UV, CD, FTIR, SEM and TEM results delineate changes in the secondary structure of xanthine oxidase. Molecular docking results provide complement to the steady-state fluorescence findings and support the view that quenching occurs due to non-polar environment experienced by aromatic residues of the enzyme. The results of this study can help scientists to tune the conformation of an enzyme (XO) with biocompatible amphiphilic microstructures, which will help to unfold further understanding in the treatment modes of various diseases like gout, hyperuricemia, liver and brain necrosis.
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Affiliation(s)
- Mohd Akram
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Imtiyaz Ahmad Bhat
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem Feeroze Bhat
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
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40
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Carvalho FAO, Alves FR, Carvalho JWP, Tabak M. Guanidine hydrochloride and urea effects upon thermal stability of Glossoscolex paulistus hemoglobin (HbGp). Int J Biol Macromol 2014; 74:18-28. [PMID: 25433131 DOI: 10.1016/j.ijbiomac.2014.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 11/16/2022]
Abstract
Glossoscolex paulistus hemoglobin (HbGp) has a molecular mass of 3600kDa. It belongs to the hexagonal bilayer hemoglobin class, which consists of highly cooperative respiratory macromolecules found in mollusks and annelids. The present work focusses on oxy-HbGp thermal stability, in the presence of urea and guanidine hydrochloride (GuHCl), monitored by several techniques. Initially, dynamic light scattering data show that the presence of GuHCl induces the protein oligomeric dissociation, followed by a significant 11-fold increase in the hydrodynamic diameter (DH) values, due to the formation of protein aggregates in solution. In contrast, urea promotes the HbGp oligomeric dissociation, followed by unfolding process at high temperatures, without aggregation. Circular dichroism data show that unfolding critical temperature (Tc) of oxy-HbGp decreases from 57°C, at 0.0 mol/L of the denaturant, to 45°C, in the presence of 3.5 mol/L of urea, suggesting the reduction of HbGp oligomeric stability. Moreover, differential scanning calorimetry results show that at lower GuHCl concentrations, some thermal stabilization of the hemoglobin is observed, whereas at higher concentrations, the reduction of stability takes place. Besides, HbGp is more stable in the presence of urea when compared with the guanidine effect, as deduced from the differences in the concentration range of denaturants.
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Affiliation(s)
| | - Fernanda R Alves
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil
| | - José W P Carvalho
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil; Universidade do Estado de Mato Grosso, MT, Brazil
| | - Marcel Tabak
- Instituto de Química de São Carlos-Universidade de São Paulo, Brazil
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41
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Xi YB, Zhao WJ, Zuo XT, Tjondro HC, Li J, Dai AB, Wang S, Yan YB. Cataract-causing mutation R233H affects the stabilities of βB1- and βA3/βB1-crystallins with different pH-dependence. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2216-29. [DOI: 10.1016/j.bbadis.2014.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 01/10/2023]
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42
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Abstract
Superfolder variant of the green fluorescent protein (sfGFP) became a favorite probe for examination of the unfolding–refolding processes of fluorescent proteins with beta-barrel structure owing to its reversible unfolding in comparison with other fluorescent proteins. Its benefit is the proper folding even in fusion constructions with poorly folded polypeptides. We noticed that guanidine thiocyanate affects not only the structure of protein but its chromophore directly. Therefore we studied the influence of ionic denaturants and salts including guanidine thiocyanate, guanidine hydrochloride, sodium chloride and sodium thiocyanate on spectral features of sfGFP. It was shown that moderate amounts of the studied agents do not disrupt sfGFP structure but provoke pronounced alteration of its spectral characteristics. Changes in absorption and CD spectra in visible spectral range indicate the specific binding of SCN− and Cl− anions in the sfGFP chromophore vicinity. The anion binding results in the redistribution of sfGFP molecules with neutral and anionic chromophores. This also hinders the proton transfer in the chromophore excited state, considerably decreasing the fluorescence intensity of sfGFP. Our results indicate that when ionic denaturants are used in the studies of fluorescent protein folding their effect on fluorophore charge state should be taken into account.
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43
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Wang Y, He H, Liu L, Gao C, Xu S, Zhao P, Xia Q. Inactivation and unfolding of protein tyrosine phosphatase from Thermus thermophilus HB27 during urea and guanidine hydrochloride denaturation. PLoS One 2014; 9:e107932. [PMID: 25255086 PMCID: PMC4177882 DOI: 10.1371/journal.pone.0107932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/18/2014] [Indexed: 11/19/2022] Open
Abstract
The effects of urea and guanidine hydrochloride (GdnHCl) on the activity, conformation and unfolding process of protein tyrosine phosphatase (PTPase), a thermostable low molecular weight protein from Thermus thermophilus HB27, have been studied. Enzymatic activity assays showed both urea and GdnHCl resulted in the inactivation of PTPase in a concentration and time-dependent manner. Inactivation kinetics analysis suggested that the inactivation of PTPase induced by urea and GdnHCl were both monophasic and reversible processes, and the effects of urea and GdnHCl on PTPase were similar to that of mixed-type reversible inhibitors. Far-ultraviolet (UV) circular dichroism (CD), Tryptophan and 1-anilinonaphthalene -8-sulfonic acid (ANS) fluorescence spectral analyses indicated the existence of a partially active and an inactive molten globule-like intermediate during the unfolding processes induced by urea and GdnHCl, respectively. Based on the sequence alignment and the homolog Tt1001 protein structure, we discussed the possible conformational transitions of PTPase induced by urea and GdnHCl and compared the conformations of these unfolding intermediates with the transient states in bovine PTPase and its complex structures in detail. Our results may be able to provide some valuable clues to reveal the relationship between the structure and enzymatic activity, and the unfolding pathway and mechanism of PTPase.
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Affiliation(s)
- Yejing Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
- College of Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Huawei He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
- College of Biotechnology, Southwest University, Beibei, Chongqing, China
- * E-mail: (QX); (HH)
| | - Lina Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Chunyan Gao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Shui Xu
- College of Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
- * E-mail: (QX); (HH)
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Stojanovski BM, Breydo L, Hunter GA, Uversky VN, Ferreira GC. Catalytically active alkaline molten globular enzyme: Effect of pH and temperature on the structural integrity of 5-aminolevulinate synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2145-54. [PMID: 25240868 DOI: 10.1016/j.bbapap.2014.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/27/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
5-Aminolevulinate synthase (ALAS), a pyridoxal-5'phosphate (PLP)-dependent enzyme, catalyzes the first step of heme biosynthesis in mammals. Circular dichroism (CD) and fluorescence spectroscopies were used to examine the effects of pH (1.0-3.0 and 7.5-10.5) and temperature (20 and 37°C) on the structural integrity of ALAS. The secondary structure, as deduced from far-UV CD, is mostly resilient to pH and temperature changes. Partial unfolding was observed at pH2.0, but further decreasing pH resulted in acid-induced refolding of the secondary structure to nearly native levels. The tertiary structure rigidity, monitored by near-UV CD, is lost under acidic and specific alkaline conditions (pH10.5 and pH9.5/37°C), where ALAS populates a molten globule state. As the enzyme becomes less structured with increased alkalinity, the chiral environment of the internal aldimine is also modified, with a shift from a 420nm to 330nm dichroic band. Under acidic conditions, the PLP cofactor dissociates from ALAS. Reaction with 8-anilino-1-naphthalenesulfonic acid corroborates increased exposure of hydrophobic clusters in the alkaline and acidic molten globules, although the reaction is more pronounced with the latter. Furthermore, quenching the intrinsic fluorescence of ALAS with acrylamide at pH1.0 and 9.5 yielded subtly different dynamic quenching constants. The alkaline molten globule state of ALAS is catalytically active (pH9.5/37°C), although the kcat value is significantly decreased. Finally, the binding of 5-aminolevulinate restricts conformational fluctuations in the alkaline molten globule. Overall, our findings prove how the structural plasticity of ALAS contributes to reaching a functional enzyme.
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Affiliation(s)
- Bosko M Stojanovski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Leonid Breydo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gregory A Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL 33612, USA; Biology Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Chemistry, University of South Florida, Tampa, FL 33612, USA.
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Crowded milieu prevents fibrillation of hen egg white lysozyme with retention of enzymatic activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:8-16. [DOI: 10.1016/j.jphotobiol.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
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46
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Bhat SA, Bano B. Conformational behaviour and aggregation of chickpea cystatin in trifluoroethanol: effects of epicatechin and tannic acid. Arch Biochem Biophys 2014; 562:51-61. [PMID: 25173679 DOI: 10.1016/j.abb.2014.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/12/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
Abstract
Conformational alterations and aggregates of chickpea cystatin (CPC) were investigated upon sequential addition of trifluoroethanol (TFE) over a range of 0-70% v/v. CPC on 30% and 40% v/v TFE addition exhibited non-native β-sheet, altered intrinsic fluorescence, increased thioflavin T fluorescence, prominent red shifted shoulder peak in Congo red absorbance, and enhanced turbidity as well as Rayleigh scattering, suggesting the aggregate formation. TEM results confirmed the formation of fibrillar aggregates at 30% and 40% v/v TFE. On increasing concentration of TFE to 70% v/v, CPC showed retention of native-like secondary structure, increased intrinsic and ANS fluorescence. Thus our results show that favourable condition for fibrillation of CPC is in the range of 30-40% TFE. Moreover, anti-aggregational effects of polyphenols, epicatechin (EC) and tannic acid (TA) were analysed using ThT binding assay and other biophysical assays. EC and TA produced a concentration dependent decline in ThT fluorescence suggesting inhibition of the fibril formation. Furthermore, TA in comparison to EC, served as a more effective inhibitor against amyloid fibril formation of CPC. This work supports the universality of the amyloid-like aggregation not restricted to some special categories of protein and the fact that this aggregation can be prevented.
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Affiliation(s)
- Sheraz Ahmad Bhat
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Bilqees Bano
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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47
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Povarova OI, Uversky VN, Kuznetsova IM, Turoverov KK. Actinous enigma or enigmatic actin: Folding, structure, and functions of the most abundant eukaryotic protein. INTRINSICALLY DISORDERED PROTEINS 2014; 2:e34500. [PMID: 28232879 PMCID: PMC5314930 DOI: 10.4161/idp.34500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 02/06/2023]
Abstract
Being the most abundant protein of the eukaryotic cell, actin continues to keep its secrets for more than 60 years. Everything about this protein, its structure, functions, and folding, is mysteriously counterintuitive, and this review represents an attempt to solve some of the riddles and conundrums commonly found in the field of actin research. In fact, actin is a promiscuous binder with a wide spectrum of biological activities. It can exist in at least three structural forms, globular, fibrillar, and inactive (G-, F-, and I-actin, respectively). G-actin represents a thermodynamically instable, quasi-stationary state, which is formed in vivo as a result of the energy-intensive, complex posttranslational folding events controlled and driven by cellular folding machinery. The G-actin structure is dependent on the ATP and Mg2+ binding (which in vitro is typically substituted by Ca2+) and protein is easily converted to the I-actin by the removal of metal ions and by action of various denaturing agents (pH, temperature, and chemical denaturants). I-actin cannot be converted back to the G-form. Foldable and “natively folded” forms of actin are always involved in interactions either with the specific protein partners, such as Hsp70 chaperone, prefoldin, and the CCT chaperonin during the actin folding in vivo or with Mg2+ and ATP as it takes place in the G-form. We emphasize that the solutions for the mysteries of actin multifunctionality, multistructurality, and trapped unfolding can be found in the quasi-stationary nature of this enigmatic protein, which clearly possesses many features attributed to both globular and intrinsically disordered proteins.
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Affiliation(s)
- Olga I Povarova
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia
| | - Vladimir N Uversky
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Russia; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia
| | - Irina M Kuznetsova
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; St. Petersburg State Polytechnical University; St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; St. Petersburg State Polytechnical University; St. Petersburg, Russia
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48
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Ghosh S, Pandey NK, Banerjee P, Chaudhury K, Nagy NV, Dasgupta S. Copper(II) directs formation of toxic amorphous aggregates resulting in inhibition of hen egg white lysozyme fibrillation under alkaline salt-mediated conditions. J Biomol Struct Dyn 2014; 33:991-1007. [PMID: 24806136 DOI: 10.1080/07391102.2014.921864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hen egg white lysozyme (HEWL) adopts a molten globule-like state at high pH (~12.75) and is found to form amyloid fibrils at alkaline pH. Here, we report that Cu(II) inhibits self-association of HEWL at pH 12.75 both at 37 and 65 °C. A significant reduction in Thioflavin T fluorescence intensity, attenuation in β-sheet content and reduction in hydrophobic exposure were observed with increasing Cu(II) stoichiometry. Electron paramagnetic resonance spectroscopy suggests a 4N type of coordination pattern around Cu(II) during fibrillation. Cu(II) is also capable of altering the cytotoxicity of the proteinaceous aggregates. Fibrillar species of diverse morphology were found in the absence of Cu(II) with the generation of amorphous aggregates in the presence of Cu(II), which are more toxic compared to the fibrils alone.
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Affiliation(s)
- Sudeshna Ghosh
- a Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
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49
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Geng HL, Bian MR, Liu Y, Cao J, Chen C, Wang ZY, Li ZY, Zeng LY, Wang XY, Wu QY, Xu KL. The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding. Int J Biol Macromol 2014; 66:302-10. [DOI: 10.1016/j.ijbiomac.2014.02.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 11/25/2022]
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50
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Stepanenko OV, Bublikov GS, Stepanenko OV, Shcherbakova DM, Verkhusha VV, Turoverov KK, Kuznetsova IM. A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome. FEBS J 2014; 281:2284-98. [PMID: 24628916 DOI: 10.1111/febs.12781] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/18/2014] [Accepted: 03/11/2014] [Indexed: 11/30/2022]
Abstract
The possibility of engineering near-infrared fluorescent proteins and biosensors from bacterial phytochrome photoreceptors (BphPs) has led to substantial interest in this family of proteins. The near-infrared fluorescent proteins have allowed non-invasive bio-imaging of deep tissues and whole organs in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called a knot, in their polypeptide chains. The formation of knot structures in proteins was refuted for a long time. Here, we studied the denaturation and renaturation processes of the near-infrared fluorescent probe iRFP, engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting efficient refolding. However, the iRFP holoform exhibited irreversible unfolding and aggregation associated with the bound chromophore. The knot structure in the apoform did not prevent subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by post-translational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are essential for future design of BphP-based near-infrared probes, and add important features to our knowledge of protein folding.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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