1
|
Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [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: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
Collapse
Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
| |
Collapse
|
2
|
Cardozo G, Mastrogiovanni M, Zeida A, Viera N, Radi R, Reyes AM, Trujillo M. Mitochondrial Peroxiredoxin 3 Is Rapidly Oxidized and Hyperoxidized by Fatty Acid Hydroperoxides. Antioxidants (Basel) 2023; 12:antiox12020408. [PMID: 36829967 PMCID: PMC9952270 DOI: 10.3390/antiox12020408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Human peroxiredoxin 3 (HsPrx3) is a thiol-based peroxidase responsible for the reduction of most hydrogen peroxide and peroxynitrite formed in mitochondria. Mitochondrial disfunction can lead to membrane lipoperoxidation, resulting in the formation of lipid-bound fatty acid hydroperoxides (LFA-OOHs) which can be released to become free fatty acid hydroperoxides (fFA-OOHs). Herein, we report that HsPrx3 is oxidized and hyperoxidized by fFA-OOHs including those derived from arachidonic acid and eicosapentaenoic acid peroxidation at position 15 with remarkably high rate constants of oxidation (>3.5 × 107 M-1s-1) and hyperoxidation (~2 × 107 M-1s-1). The endoperoxide-hydroperoxide PGG2, an intermediate in prostanoid synthesis, oxidized HsPrx3 with a similar rate constant, but was less effective in causing hyperoxidation. Biophysical methodologies suggest that HsPrx3 can bind hydrophobic structures. Indeed, molecular dynamic simulations allowed the identification of a hydrophobic patch near the enzyme active site that can allocate the hydroperoxide group of fFA-OOHs in close proximity to the thiolate in the peroxidatic cysteine. Simulations performed using available and herein reported kinetic data indicate that HsPrx3 should be considered a main target for mitochondrial fFA-OOHs. Finally, kinetic simulation analysis support that mitochondrial fFA-OOHs formation fluxes in the range of nM/s are expected to contribute to HsPrx3 hyperoxidation, a modification that has been detected in vivo under physiological and pathological conditions.
Collapse
Affiliation(s)
- Giuliana Cardozo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Nicolás Viera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Aníbal M. Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
| |
Collapse
|
3
|
Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
| |
Collapse
|
4
|
Permyakov SE, Yundina EN, Kazakov AS, Permyakova ME, Uversky VN, Permyakov EA. Mouse S100G protein exhibits properties characteristic of a calcium sensor. Cell Calcium 2020; 87:102185. [PMID: 32114281 DOI: 10.1016/j.ceca.2020.102185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 01/09/2023]
Abstract
Bovine S100 G (calbindin D9k, small Ca2+-binding protein of the EF-hand superfamily) is considered as a calcium buffer protein; i.e., the binding of Ca2+ practically does not change its general conformation. A set of experimental approaches has been used to study structural properties of apo- and Ca2+-loaded forms of mouse S100 G (81.4% identity in amino acid sequence with bovine S100 G). This analysis revealed that, in contrast to bovine S100 G, the removal of calcium ions increases α-helices content of mouse S100 G protein and enhances its accessibility to digestion by α-chymotrypsin. Furthermore, mouse apo-S100 G is characterized by a decreased surface hydrophobicity and reduced tendency for oligomerization. Such behavior is typical of calcium sensor proteins. Apo-state of mouse S100 G still has rather compact structure, which can be cooperatively unfolded by temperature and GdnHCl. Computational analysis of amino acid sequences of S100 G proteins shows that these proteins could be in a disordered state upon a removal of the bound calcium ions. The experimental data show that, although mouse apo-S100 G is flexible compared to the Ca2+-loaded state, the apo-form is not completely disordered and preserves some cooperatively meting structure. The origin of the unexpectedly high stability of mouse S100 G can be rationalized by an exceptionally strong association of its N- and C-terminal parts containing the EF-hands I and II, respectively.
Collapse
Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Elena N Yundina
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| |
Collapse
|
5
|
Sulatsky MI, Sulatskaya AI, Povarova OI, Antifeeva IA, Kuznetsova IM, Turoverov KK. Effect of the fluorescent probes ThT and ANS on the mature amyloid fibrils. Prion 2020; 14:67-75. [PMID: 32008441 PMCID: PMC7009331 DOI: 10.1080/19336896.2020.1720487] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fluorescent probes thioflavin T (ThT) and 1-anilino-8-naphthalene sulfonate (ANS) are widely used to study amyloid fibrils that accumulate in the body of patients with serious diseases, such as Alzheimer’s, Parkinson’s, prion diseases, etc. However, the possible effect of these probes on amyloid fibrils is not well understood. In this work, we investigated the photophysical characteristics, structure, and morphology of mature amyloid fibrils formed from two model proteins, insulin and lysozyme, in the presence of ThT and ANS. It turned out that ANS affects the secondary structure of amyloids (shown for fibrils formed from insulin and lysozyme) and their fibers clusterization (valid for lysozyme fibrils), while ThT has no such effects. These results confirm the differences in the mechanisms of these dyes interaction with amyloid fibrils. Observed effect of ANS was explained by the electrostatic interactions between the dye molecule and cationic groups of amyloid-forming proteins (unlike hydrophobic binding of ThT) that induce amyloids conformational changes. This interaction leads to weakening repulsion between positive charges of amyloid fibrils and can promote their clusterization. It was shown that when fibrillogenesis conditions and, consequently, fibrils structure is changing, as well as during defragmentation of amyloids by ultrasonication, the influence of ANS to amyloids does not change, which indicates the universality of the detected effects. Based on the obtained results, it was concluded that ANS should be used cautiously for the study of amyloid fibrils, since this fluorescence probe have a direct effect on the object of study.
Collapse
Affiliation(s)
- M I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - A I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - O I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - Iu A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - I M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - K K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia.,Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| |
Collapse
|
6
|
Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
Collapse
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
| |
Collapse
|
7
|
Joseph A, Nagaraja V, Natesh R. Mycobacterial transcript cleavage factor Gre, exhibits chaperone-like activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:757-764. [PMID: 31125617 DOI: 10.1016/j.bbapap.2019.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 02/05/2023]
Abstract
Gre factors reactivate stalled elongation complexes by enhancing the intrinsic transcript cleavage activity of RNA polymerase. Previous work by us has shown that unlike in Escherichia coli (E.coli), Mycobacterium tuberculosis Gre factor is essential for its survival. Apart from their role in transcription regulation Gre factors have been implicated in stress response. A recent study has shown the role of E.coli GreA as a cellular chaperone, which inhibits aggregation of substrate proteins under heat stress condition. Moreover it was shown that GreA enables E.coli to survive heat shock and oxidative stress. In the current work, we have characterized the moonlighting chaperone activity and its plausible mechanism in Mycobacterium smegmatis Gre (MsGre) factor. We show here that MsGre prevents heat-induced aggregation of the substrate protein and also protects enzymatic activity. Interestingly Gre factor exists as a dimer in solution and does not undergo heat induced oligomerization. From the 8-anilino-1-naphthalene sulfonate (ANS) binding studies MsGre was shown to expose hydrophobic surface upon heat stress that would allow binding to unfolded or partially folded substrate protein. From Circular Dichroism (CD) studies, we also show that MsGre has a stable secondary structure under thermal stress. We propose that the presence of C-terminal FKBP-like fold in MsGre factor that might contribute to its chaperone-like function.
Collapse
Affiliation(s)
- Abyson Joseph
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Trivandrum, Kerala 695551, India
| | - Valakunja Nagaraja
- Microbiology and Cell Biology Unit, Indian Institute of Science, Bangalore, Karnataka, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Ramanathan Natesh
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Trivandrum, Kerala 695551, India.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Permyakova ME, Permyakov SE, Kazakov AS, Denesyuk AI, Denessiouk K, Uversky VN, Permyakov EA. Analyzing the structural and functional roles of residues from the 'black' and 'gray' clusters of human S100P protein. Cell Calcium 2019; 80:46-55. [PMID: 30953998 DOI: 10.1016/j.ceca.2019.03.008] [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: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
Two highly conserved structural motifs observed in members of the EF-hand family of calcium binding proteins. The motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif represents a cluster of three amino acids called cluster I ('black' cluster) and cluster II ('grey' cluster). Cluster I is more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II is noticeably less conserved and includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. In the human calcium binding S100 P protein, these 'black' and 'gray' clusters include residues F15, F71, and F74 and L33, L58, and K30, respectively. To evaluate the effects of these clusters on structure and functionality of human S100 P, we have performed Ala scanning. The resulting mutants were studied by a multiparametric approach that included circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probes. Spectrofluorimetric Ca2+-titration of wild type S100 P showed that S100 P dimer has 1-2 strong calcium binding sites (K1 = 4 × 106 M-1) and two cooperative low affinity (K2 = 4 × 104 M-1) binding sites. Similarly, the S100 P mutants possess two types of calcium binding sites. This analysis revealed that the alanine substitutions in the clusters I and II caused comparable changes in the S100 P functional properties. However, analysis of heat- or GuHCl-induced unfolding of these proteins showed that the alanine substitutions in the cluster I caused notably more pronounced decrease in the protein stability compared to the changes caused by alanine substitutions in the cluster II. Opposite to literature data, the F15 A substitution did not cause the S100 P dimer dissociation, indicating that F15 is not crucial for dimer stability. Overall, similar to parvalbumins, the S100 P cluster I is more important for protein conformational stability than the cluster II.
Collapse
Affiliation(s)
- Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia.
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
| | - Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland; Pharmaceutical Sciences Laboratory, Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
| |
Collapse
|
10
|
Permyakov SE, Vologzhannikova AA, Khorn PA, Shevelyova MP, Kazakov AS, Emelyanenko VI, Denesyuk AI, Denessiouk K, Uversky VN, Permyakov EA. Comprehensive analysis of the roles of 'black' and 'gray' clusters in structure and function of rat β-parvalbumin. Cell Calcium 2018; 75:64-78. [PMID: 30176502 DOI: 10.1016/j.ceca.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/26/2018] [Indexed: 01/05/2023]
Abstract
Recently we found two highly conserved structural motifs in the proteins of the EF-hand calcium binding protein family. These motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif forms a cluster of three amino acids called cluster I ('black' cluster) and cluster II ('grey' cluster). Cluster I is much more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II includes a mix of aromatic, hydrophobic, and polar amino acids. The 'black' and 'gray' clusters in rat β-parvalbumin consist of F48, A100, F103 and G61, L64, M87, respectively. In the present work, we sequentially substituted these amino acids residues by Ala, except Ala100, which was substituted by Val. Physical properties of the mutants were studied by circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probe methods. The Ca2+ and Mg2+ binding affinities of these mutants were evaluated by intrinsic fluorescence and equilibrium dialysis methods. In spite of a rather complicated pattern of contributions of separate amino acid residues of the 'black' and 'gray' clusters into maintenance of rat β-parvalbumin structural and functional status, the alanine substitutions in the cluster I cause noticeably more pronounced changes in various structural parameters of proteins, such as hydrodynamic radius of apo-form, thermal stability of Ca2+/Mg2+-loaded forms, and total energy of Ca2+ binding in comparison with the changes caused by amino acid substitutions in the cluster II. These findings were further supported by the outputs of computational analysis of the effects of these mutations on the intrinsic disorder predisposition of rat β-parvalbumin, which also indicated that local intrinsic disorder propensities and the overall levels of predicted disorder were strongly affected by mutations in the cluster I, whereas mutations in cluster II had less pronounced effects. These results demonstrate that amino acids of the cluster I provide more essential contribution to the maintenance of structuraland functional properties of the protein in comparison with the residues of the cluster II.
Collapse
Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alisa A Vologzhannikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Polina A Khorn
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Marina P Shevelyova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Victor I Emelyanenko
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland; Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russia
| |
Collapse
|
11
|
Nemergut M, Žoldák G, Schaefer JV, Kast F, Miškovský P, Plückthun A, Sedlák E. Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering. Protein Sci 2017; 26:2229-2239. [PMID: 28833802 DOI: 10.1002/pro.3278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies of the immunoglobulin G (IgG) type have become mainstream therapeutics for the treatment of many life-threatening diseases. For their successful application in the clinic and a favorable cost-benefit ratio, the design and formulation of these therapeutic molecules must guarantee long-term stability for an extended period of time. Accelerated stability studies, e.g., by employing thermal denaturation, have the great potential for enabling high-throughput screening campaigns to find optimal molecular variants and formulations in a short time. Surprisingly, no validated quantitative analysis of these accelerated studies has been performed yet, which clearly limits their application for predicting IgG stability. Therefore, we have established a quantitative approach for the assessment of the kinetic stability over a broad range of temperatures. To this end, differential scanning calorimetry (DSC) experiments were performed with a model IgG, testing chaotropic formulations and an extended temperature range, and they were subsequently analyzed by our recently developed three-step sequential model of IgG denaturation, consisting of one reversible and two irreversible steps. A critical comparison of the predictions from this model with data obtained by an orthogonal fluorescence probe method, based on 8-anilinonaphthalene-1-sulfonate binding to partially unfolded states, resulted in very good agreement. In summary, our study highlights the validity of this easy-to-perform analysis for reliably assessing the kinetic stability of IgGs, which can support accelerated formulation development of monoclonal antibodies by ranking different formulations as well as by improving colloidal stability models.
Collapse
Affiliation(s)
- Michal Nemergut
- Department of Biophysics, P.J. Šafárik University, Jesenna 5, Košice, 041 54, Slovakia
| | - Gabriel Žoldák
- Department of Biophysics, Institute of Molecular and Cellular Biophysics, Technical University of Munich, James-Franck-Str. 1, Garching, D-85748, Germany
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Florian Kast
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Pavol Miškovský
- Department of Biophysics, P.J. Šafárik University, Jesenna 5, Košice, 041 54, Slovakia.,Centre for Interdisciplinary Biosciences, P.J. Šafárik University, Jesenna 5, Košice, 041 54, Slovakia
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P.J. Šafárik University, Jesenna 5, Košice, 041 54, Slovakia.,Department of Biochemistry, P.J. Šafárik University, Moyzesova 11, Košice, 040 01, Slovakia
| |
Collapse
|
12
|
de Souza TLF, de Lima SMB, Braga VLDA, Peabody DS, Ferreira DF, Bianconi ML, Gomes AMDO, Silva JL, de Oliveira AC. Charge neutralization as the major factor for the assembly of nucleocapsid-like particles from C-terminal truncated hepatitis C virus core protein. PeerJ 2016; 4:e2670. [PMID: 27867765 PMCID: PMC5111903 DOI: 10.7717/peerj.2670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/08/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) core protein, in addition to its structural role to form the nucleocapsid assembly, plays a critical role in HCV pathogenesis by interfering in several cellular processes, including microRNA and mRNA homeostasis. The C-terminal truncated HCV core protein (C124) is intrinsically unstructured in solution and is able to interact with unspecific nucleic acids, in the micromolar range, and to assemble into nucleocapsid-like particles (NLPs) in vitro. The specificity and propensity of C124 to the assembly and its implications on HCV pathogenesis are not well understood. METHODS Spectroscopic techniques, transmission electron microscopy and calorimetry were used to better understand the propensity of C124 to fold or to multimerize into NLPs when subjected to different conditions or in the presence of unspecific nucleic acids of equivalent size to cellular microRNAs. RESULTS The structural analysis indicated that C124 has low propensity to self-folding. On the other hand, for the first time, we show that C124, in the absence of nucleic acids, multimerizes into empty NLPs when subjected to a pH close to its isoelectric point (pH ≈ 12), indicating that assembly is mainly driven by charge neutralization. Isothermal calorimetry data showed that the assembly of NLPs promoted by nucleic acids is enthalpy driven. Additionally, data obtained from fluorescence correlation spectroscopy show that C124, in nanomolar range, was able to interact and to sequester a large number of short unspecific nucleic acids into NLPs. DISCUSSION Together, our data showed that the charge neutralization is the major factor for the nucleocapsid-like particles assembly from C-terminal truncated HCV core protein. This finding suggests that HCV core protein may physically interact with unspecific cellular polyanions, which may correspond to microRNAs and mRNAs in a host cell infected by HCV, triggering their confinement into infectious particles.
Collapse
Affiliation(s)
- Theo Luiz Ferraz de Souza
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Vanessa L. de Azevedo Braga
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - David S. Peabody
- Department of Molecular Genetics and Microbiology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, United States
| | - Davis Fernandes Ferreira
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M. Lucia Bianconi
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andre Marco de Oliveira Gomes
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jerson Lima Silva
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andréa Cheble de Oliveira
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
13
|
Insights into the structure-function relationship of Brugia malayi thymidylate kinase (BmTMK). Int J Biol Macromol 2016; 88:565-71. [PMID: 27044348 DOI: 10.1016/j.ijbiomac.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 11/23/2022]
Abstract
Lymphatic filariasis is a debilitating disease caused by lymph dwelling nematodal parasites like Wuchereria bancrofti, Brugia malayi and Brugia timori. Thymidylate kinase of B. malayi is a key enzyme in the de novo and salvage pathways for thymidine 5'-triphosphate (dTTP) synthesis. Therefore, B. malayi thymidylate kinase (BmTMK) is an essential enzyme for DNA biosynthesis and an important drug target to rein in filariasis. In the present study, the structural and functional changes associated with recombinant BmTMK, in the presence of protein denaturant GdnHCl, urea and pH were studied. GdnHCl and urea induced unfolding of BmTMK is non-cooperative and influence the functional property of the enzyme much lower than their Cm values. The study delineate that BmTMK is more prone to ionic perturbation. The dimeric assembly of BmTMK is an absolute requirement for enzymatic acitivity and any subtle change in dimeric conformation due to denaturation leads to loss of enzymatic activity. The pH induced changes on structure and activity suggests that selective modification of active site microenvironment pertains to difference in activity profile. This study also envisages that chemical moieties which acts by modulating oligomeric assembly, could be used for better designing of inhibitors against BmTMK enzyme.
Collapse
|
14
|
Roychaudhuri R, Zheng X, Lomakin A, Maiti P, Condron MM, Benedek GB, Bitan G, Bowers MT, Teplow DB. Role of Species-Specific Primary Structure Differences in Aβ42 Assembly and Neurotoxicity. ACS Chem Neurosci 2015; 6:1941-55. [PMID: 26421877 PMCID: PMC4844016 DOI: 10.1021/acschemneuro.5b00180] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A variety of species express the amyloid β-protein (Aβ (the term "Aβ" refers both to Aβ40 and Aβ42, whereas "Aβ40" and "Aβ42" refer to each isoform specifically). Those species expressing Aβ with primary structure identical to that expressed in humans have been found to develop amyloid deposits and Alzheimer's disease-like neuropathology. In contrast, the Aβ sequence in mice and rats contains three amino acid substitutions, Arg5Gly, His13Arg, and Tyr10Phe, which apparently prevent the development of AD-like neuropathology. Interestingly, the brush-tailed rat, Octodon degus, expresses Aβ containing only one of these substitutions, His13Arg, and does develop AD-like pathology. We investigate here the biophysical and biological properties of Aβ peptides from humans, mice (Mus musculus), and rats (Octodon degus). We find that each peptide displays statistical coil → β-sheet secondary structure transitions, transitory formation of hydrophobic surfaces, oligomerization, formation of annuli, protofibrils, and fibrils, and an inverse correlation between rate of aggregation and aggregate size (faster aggregation produced smaller aggregates). The rank order of assembly rate was mouse > rat > Aβ42. The rank order of neurotoxicity of assemblies formed by each peptide immediately after preparation was Aβ42 > mouse ≈ rat. These data do not support long-standing hypotheses that the primary factor controlling development of AD-like neuropathology in rodents is Aβ sequence. Instead, the data support a hypothesis that assembly quaternary structure and organismal responses to toxic peptide assemblies mediate neuropathogenetic effects. The implication of this hypothesis is that a valid understanding of disease causation within a given system (organism, tissue, etc.) requires the coevaluation of both biophysical and cell biological properties of that system.
Collapse
Affiliation(s)
- Robin Roychaudhuri
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Xueyun Zheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Aleksey Lomakin
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Panchanan Maiti
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Margaret M. Condron
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - George B. Benedek
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
| |
Collapse
|
15
|
Xiao QJ, Li ZG, Yang J, He Q, Xi L, Du LF. Heat-induced unfolding of apo-CP43 studied by fluorescence spectroscopy and CD spectroscopy. PHOTOSYNTHESIS RESEARCH 2015; 126:427-435. [PMID: 26071019 DOI: 10.1007/s11120-015-0166-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
CP43 is a chlorophyll-binding protein, which acts as a conduit for the excitation energy transfer. The thermal stability of apo-CP43 was studied by intrinsic fluorescence, exogenous ANS fluorescence, and circular dichroism spectroscopy. Under heat treatment, the structure of apo-CP43 changed and existed transition state occurred between 56 and 62 °C by the intrinsic, exogenous ANS fluorescence and the analysis of hydrophobicity. Besides, the isosbestic point of the sigmoidal curve was 58.10 ± 1.02 °C by calculating α-helix transition and the Tm was 56.45 ± 0.52 and 55.59 ± 0.68 °C by calculating the unfolded fraction of tryptophan and tyrosine fluorescence, respectively. During the process of unfolding, the hydrophobic structure of C-terminal segment firstly started to expose at 40 °C, and then the hydrophobic cluster adjacent to the N-terminal segment also gradually exposed to hydrophilic environment with increasing temperature. Our results indicated that heat treatment, especially above 40 °C, has an important impact on the structural stability of apo-CP43.
Collapse
Affiliation(s)
- Qing-Jie Xiao
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zai-Geng Li
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jiao Yang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Qing He
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Lei Xi
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Lin-Fang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
| |
Collapse
|
16
|
Zeida A, Reyes AM, Lichtig P, Hugo M, Vazquez DS, Santos J, González Flecha FL, Radi R, Estrin DA, Trujillo M. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis. Biochemistry 2015; 54:7237-47. [DOI: 10.1021/acs.biochem.5b00758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aníbal M. Reyes
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Martín Hugo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | | | | | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Madia Trujillo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| |
Collapse
|
17
|
Bhattacharya A, Ray S, Singh D, Dhaked HPS, Panda D. ZapC promotes assembly and stability of FtsZ filaments by binding at a different site on FtsZ than ZipA. Int J Biol Macromol 2015; 81:435-42. [DOI: 10.1016/j.ijbiomac.2015.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 12/27/2022]
|
18
|
Yang M, Dutta C, Tiwari A. Disulfide-bond scrambling promotes amorphous aggregates in lysozyme and bovine serum albumin. J Phys Chem B 2015; 119:3969-81. [PMID: 25689578 DOI: 10.1021/acs.jpcb.5b00144] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Disulfide bonds are naturally formed in more than 50% of amyloidogenic proteins, but the exact role of disulfide bonds in protein aggregation is still not well-understood. The intracellular reducing agents and/or improper use of antioxidants in extracellular environment can break proteins disulfide bonds, making them unstable and prone to misfolding and aggregation. In this study, we report the effect of disulfide-reducing agent dithiothreitol (DTT) on hen egg white lysozyme (lysozyme) and bovine serum albumin (BSA) aggregation at pH 7.2 and 37 °C. BSA and lysozyme proteins treated with disulfide-reducing agents form very distinct amorphous aggregates as observed by scanning electron microscope. However, proteins with intact disulfide bonds were stable and did not aggregate over time. BSA and lysozyme aggregates show unique but measurable differences in 8-anilino-1-naphthalenesulfonic acid (ANS) and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) fluorescence, suggesting a loose and flexible aggregate structure for lysozyme but a more compact aggregate structure for BSA. Scrambled disulfide-bonded protein aggregates were observed by nonreducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) for both proteins. Similar amorphous aggregates were also generated using a nonthiol-based reducing agent, tris(2-carboxyethyl)phosphine (TCEP), at pH 7.2 and 37 °C. In summary, formation of distinct amorphous aggregates by disulfide-reduced BSA and lysozyme suggests an alternate pathway for protein aggregation that may be relevant to several proteins.
Collapse
Affiliation(s)
- Mu Yang
- Department of Chemistry, Michigan Technological University , Houghton, Michigan 49931, United States
| | | | | |
Collapse
|
19
|
DiMauro MA, Nandi SK, Raghavan CT, Kar RK, Wang B, Bhunia A, Nagaraj RH, Biswas A. Acetylation of Gly1 and Lys2 promotes aggregation of human γD-crystallin. Biochemistry 2014; 53:7269-82. [PMID: 25393041 PMCID: PMC4245984 DOI: 10.1021/bi501004y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
The human lens contains three major
protein families: α-,
β-, and γ-crystallin. Among the several variants of γ-crystallin
in the human lens, γD-crystallin is a major form. γD-Crystallin
is primarily present in the nuclear region of the lens and contains
a single lysine residue at the second position (K2). In this study,
we investigated the acetylation of K2 in γD-crystallin in aging
and cataractous human lenses. Our results indicated that K2 is acetylated
at an early age and that the amount of K2-acetylated γD-crystallin
increased with age. Mass spectrometric analysis revealed that in addition
to K2, glycine 1 (G1) was acetylated in γD-crystallin from human
lenses and in γD-crystallin acetylated in vitro. The chaperone ability of α-crystallin for acetylated γD-crystallin
was lower than that for the nonacetylated protein. The tertiary structure
and the microenvironment of the cysteine residues were significantly
altered by acetylation. The acetylated protein exhibited higher surface
hydrophobicity, was unstable against thermal and chemical denaturation,
and exhibited a higher propensity to aggregate at 80 °C in comparison
to the nonacetylated protein. Acetylation enhanced the GdnHCl-induced
unfolding and slowed the subsequent refolding of γD-crystallin.
Theoretical analysis indicated that the acetylation of K2 and G1 reduced
the structural stability of the protein and brought the distal cysteine
residues (C18 and C78) into close proximity. Collectively, these results
indicate that the acetylation of G1 and K2 residues in γD-crystallin
likely induced a molten globule-like structure, predisposing it to
aggregation, which may account for the high content of aggregated
proteins in the nucleus of aged and cataractous human lenses.
Collapse
Affiliation(s)
- Michael A DiMauro
- Department of Ophthalmology and Visual Sciences and ‡Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine , Cleveland, Ohio, United States
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Araujo TLS, Borges JC, Ramos CH, Meyer-Fernandes JR, Oliveira Júnior RS, Pascutti PG, Foguel D, Palhano FL. Conformational changes in human Hsp70 induced by high hydrostatic pressure produce oligomers with ATPase activity but without chaperone activity. Biochemistry 2014; 53:2884-9. [PMID: 24739062 DOI: 10.1021/bi500004q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the folding of the 70 kDa human cytosolic inducible protein (Hsp70) in vitro using high hydrostatic pressure as a denaturing agent. We followed the structural changes in Hsp70 induced by high hydrostatic pressure using tryptophan fluorescence, molecular dynamics, circular dichroism, high-performance liquid chromatography gel filtration, dynamic light scattering, ATPase activity, and chaperone activity. Although monomeric, Hsp70 is very sensitive to hydrostatic pressure; after pressure had been removed, the protein did not return to its native sate but instead formed oligomeric species that lost chaperone activity but retained ATPase activity.
Collapse
Affiliation(s)
- Thaís L S Araujo
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-590, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Park CH, Lee SS, Kim KR, Jung MH, Lee SY, Cho EJ, Singh S, Chung BY. Optimized enzymatic dual functions of PaPrx protein by proton irradiation. JOURNAL OF RADIATION RESEARCH 2014; 55:17-24. [PMID: 23753570 PMCID: PMC3885114 DOI: 10.1093/jrr/rrt081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We investigated the effects of proton irradiation on the function and structure of the Pseudomonas aeruginosa peroxiredoxin (PaPrx). Polyacrylamide gel demonstrated that PaPrx proteins exposed to proton irradiation at several doses exhibited simultaneous formation of high molecular weight (HMW) complexes and fragmentation. Size-exclusion chromatography (SEC) analysis revealed that the number of fragments and very low molecular weight (LMW) structures increased as the proton irradiation dose increased. The peroxidase activity of irradiated PaPrx was preserved, and its chaperone activity was significantly increased by increasing the proton irradiation dose. The chaperone activity increased about 3-4 fold after 2.5 kGy proton irradiation, compared with that of non-irradiated PaPrx, and increased to almost the maximum activity after 10 kGy proton irradiation. We previously obtained functional switching in PaPrx proteins, by using gamma rays and electron beams as radiation sources, and found that the proteins exhibited increased chaperone activity but decreased peroxidase activity. Interestingly, in this study we newly found that proton irradiation could enhance both peroxidase and chaperone activities. Therefore, we can suggest proton irradiation as a novel protocol for conserved 2-Cys protein engineering.
Collapse
Affiliation(s)
- Chul-Hong Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Kye Ryung Kim
- Proton Engineering Frontier Project, Korea Atomic Energy Research Institute, Gyeongju 780-904, Republic of Korea
| | - Myung Hwan Jung
- Proton Engineering Frontier Project, Korea Atomic Energy Research Institute, Gyeongju 780-904, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Eun Ju Cho
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sudhir Singh
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
- Corresponding author. Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup 580-185, Republic of Korea. Tel: +82-63-570-3331; Fax: +82-63-570-3339;
| |
Collapse
|
22
|
Lin PY, Simon SM, Koh WK, Folorunso O, Umbaugh CS, Pierce A. Heat shock factor 1 over-expression protects against exposure of hydrophobic residues on mutant SOD1 and early mortality in a mouse model of amyotrophic lateral sclerosis. Mol Neurodegener 2013; 8:43. [PMID: 24256636 PMCID: PMC3907013 DOI: 10.1186/1750-1326-8-43] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 11/11/2013] [Indexed: 12/13/2022] Open
Abstract
Background Mutations in the Cu/Zn superoxide dismutase gene (SOD1) are responsible for 20% of familial forms of amyotrophic lateral sclerosis (ALS), and mutant SOD1 has been shown to have increased surface hydrophobicity in vitro. Mutant SOD1 may adopt a complex array of conformations with varying toxicity in vivo. We have used a novel florescence-based proteomic assay using 4,4’-bis-1-anilinonaphthalene-8-sulfonate (bisANS) to assess the surface hydrophobicity, and thereby distinguish between different conformations, of SOD1and other proteins in situ. Results Covalent bisANS labeling of spinal cord extracts revealed that alterations in surface hydrophobicity of H46R/H48Q mutations in SOD1 provoke formation of high molecular weight SOD1 species with lowered solubility, likely due to increased exposure of hydrophobic surfaces. BisANS was docked on the H46R/H48Q SOD1 structure at the disordered copper binding and electrostatic loops of mutant SOD1, but not non-mutant WT SOD1. 16 non-SOD1 proteins were also identified that exhibited altered surface hydrophobicity in the H46R/H48Q mutant mouse model of ALS, including proteins involved in energy metabolism, cytoskeleton, signaling, and protein quality control. Heat shock proteins (HSPs) were also enriched in the detergent-insoluble fractions with SOD1. Given that chaperones recognize proteins with exposed hydrophobic surfaces as substrates and the importance of protein homeostasis in ALS, we crossed SOD1 H46R/H48Q mutant mice with mice over-expressing the heat shock factor 1 (HSF1) transcription factor. Here we showed that HSF1 over-expression in H46R/H48Q ALS mice enhanced proteostasis as evidenced by increased expression of HSPs in motor neurons and astrocytes and increased solubility of mutant SOD1. HSF1 over-expression significantly reduced body weight loss, delayed ALS disease onset, decreases cases of early disease, and increased survival for the 25th percentile in an H46R/H48Q SOD1 background. HSF1 overexpression did not affect macroautophagy in the ALS background, but was associated with maintenance of carboxyl terminus of Hsp70 interacting protein (CHIP) expression which declined in H46R/H48Q mice. Conclusion Our results uncover the potential importance of changes in protein surface hydrophobicity of SOD1 and other non-SOD1 proteins in ALS, and how strategies that activate HSF1 are valid therapies for ALS and other age-associated proteinopathies.
Collapse
Affiliation(s)
- Pei-Yi Lin
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | | | | | | | | | | |
Collapse
|
23
|
Chen G, Zwart PH, Li D. Component particle structure in heterogeneous disordered ensembles extracted from high-throughput fluctuation x-ray scattering. PHYSICAL REVIEW LETTERS 2013; 110:195501. [PMID: 23705716 DOI: 10.1103/physrevlett.110.195501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Indexed: 06/02/2023]
Abstract
The ring angular correlation function is a characteristic feature determined by the particle structure. Averaging over a large number of ring angular correlation functions calculated from x-ray diffraction patterns will cancel out the cross correlations between different particles and converge to the autocorrelation functions of single particles. Applied on heterogeneous disordered ensembles, the retrieved function is a linear combination of a single-particle autocorrelation function multiplied by the molar ratios in a heterogeneous system. Using this relation, the ring angular correlation functions of the individual component particles in the heterogeneous system can be retrieved through the high throughput fluctuation x-ray scattering technique. This method is demonstrated with a simulated heterogeneous system composed of nanorods, nanoprism, and nanorice.
Collapse
Affiliation(s)
- Gang Chen
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China.
| | | | | |
Collapse
|
24
|
An BC, Lee SS, Lee JT, Park CH, Lee SY, Chung BY. Change in the enzymatic dual function of the peroxiredoxin protein by gamma irradiation. Radiat Phys Chem Oxf Engl 1993 2012. [DOI: 10.1016/j.radphyschem.2012.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
25
|
ZipA binds to FtsZ with high affinity and enhances the stability of FtsZ protofilaments. PLoS One 2011; 6:e28262. [PMID: 22164258 PMCID: PMC3229571 DOI: 10.1371/journal.pone.0028262] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/04/2011] [Indexed: 11/19/2022] Open
Abstract
A bacterial membrane protein ZipA that tethers FtsZ to the membrane is known to promote FtsZ assembly. In this study, the binding of ZipA to FtsZ was monitored using fluorescence spectroscopy. ZipA was found to bind to FtsZ with high affinities at three different (6.0, 6.8 and 8.0) pHs, albeit the binding affinity decreased with increasing pH. Further, thick bundles of FtsZ protofilaments were observed in the presence of ZipA under the pH conditions used in this study indicating that ZipA can promote FtsZ assembly and stabilize FtsZ polymers under unfavorable conditions. Bis-ANS, a hydrophobic probe, decreased the interaction of FtsZ and ZipA indicating that the interaction between FtsZ and ZipA is hydrophobic in nature. ZipA prevented the dilution induced disassembly of FtsZ polymers suggesting that it stabilizes FtsZ protofilaments. Fluorescein isothiocyanate-labeled ZipA was found to be uniformly distributed along the length of the FtsZ protofilaments indicating that ZipA stabilizes FtsZ protofilaments by cross-linking them.
Collapse
|
26
|
An BC, Lee SS, Lee JT, Hong SH, Wi SG, Chung BY. Engineering of 2-Cys peroxiredoxin for enhanced stress-tolerance. Mol Cells 2011; 32:257-64. [PMID: 21773675 PMCID: PMC3887637 DOI: 10.1007/s10059-011-1047-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/13/2011] [Accepted: 06/13/2011] [Indexed: 10/18/2022] Open
Abstract
A typical 2-cysteine peroxiredoxin (2-Cys Prx)-like protein (PpPrx) that alternatively acts as a peroxidase or a molecular chaperone in Pseudomonas putida KT2440 was previously characterized. The dual functions of PpPrx are regulated by the existence of an additional Cys(112) between the active Cys(51) and Cys(171) residues. In the present study, additional Cys residues (Cys(31), Cys(112), and Cys(192)) were added to PpPrx variants to improve their enzymatic function. The optimal position of the additional Cys residues for the dual functionality was assessed. The peroxidase activities of the S31C and Y192C mutants were increased 3- to 4-fold compared to the wild-type, while the chaperone activity was maintained at > 66% of PpPrx. To investigate whether optimization of the dual functions could enhance stress-tolerance in vivo, a complementation study was performed. The S31C and Y192C mutants showed a much greater tolerance than other variants under a complex condition of heat and oxidative stresses. The optimized dual functions of PpPrx could be adapted for use in bioengineering systems and industries, such as to develop organisms that are more resistant to extreme environments.
Collapse
Affiliation(s)
| | | | | | | | - Seung Gon Wi
- Bio-Energy Research Institute, Chonnam National University, Gwangju 500-757, Korea
| | | |
Collapse
|
27
|
Zakharov MN, Ulloor J, Bhasin S, Ross JA, Narula NS, Bakhit M, Pillai BK, Kumar R, Jameson DM, Jasuja R. Guanidinium chloride-induced spectral perturbations of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid confound interpretation of data on molten globule states. Anal Biochem 2011; 416:126-8. [PMID: 21569754 DOI: 10.1016/j.ab.2011.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/09/2011] [Accepted: 04/12/2011] [Indexed: 11/18/2022]
Abstract
We describe limitations in the use of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to examine unfolding intermediates associated with guanidinium chloride (GuHCl)-induced protein denaturation. Several studies have used alterations in fluorescence emission of bis-ANS to quantify the population of "molten globule" states. Our findings indicate that the observed changes in bis-ANS spectroscopic properties could originate from the interactions of bis-ANS and GuHCl and the aggregation of the dye at higher GuHCl concentrations. We posit that in the absence of additional complementary structural or spectroscopic measurements, the use of bis-ANS emission alone to monitor protein conformations can be misleading.
Collapse
Affiliation(s)
- M N Zakharov
- Section of Endocrinology, Diabetes, and Nutrition, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Chatterjee T, Mukherjee D, Dey S, Pal A, Hoque KM, Chakrabarti P. Accessory cholera enterotoxin, Ace, from Vibrio cholerae: structure, unfolding, and virstatin binding. Biochemistry 2011; 50:2962-72. [PMID: 21366345 DOI: 10.1021/bi101673x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrio cholerae accessory cholera enterotoxin (Ace) is the third toxin, along with cholera toxin (CT) and zonula occludens toxin (Zot), that causes the endemic disease cholera. Structural characterization of Ace has been restricted because of the limited production of this toxic protein by V. cholerae. We have cloned, overexpressed, and purified Ace from V. cholerae strain O395 in Escherichia coli to homogeneity and determined its biological activity. The unfolding of the purified protein was investigated using circular dichroism and intrinsic tryptophan fluorescence. Because Ace is predominantly a hydrophobic protein, the degree of exposure of hydrophobic regions was identified from the spectral changes of the environment-sensitive fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) that quenches the fluorescence of tryptophan residues of Ace in a concentration-dependent manner. Results showed that bis-ANS binds one monomeric unit of Ace with a 1:1 stoichiometry and a K' of 0.72 μM. Ace exists as a dimer, with higher oligomeric forms appearing upon glutaraldehyde cross-linking. This study also reports the binding of virstatin, a small molecule that inhibits virulence regulation in V. cholerae, to Ace. The binding constant (K=9×10(4) M(-1)) and the standard free energy change (ΔG°=-12 kcal mol(-1)) of Ace-virstatin interaction have been evaluated by the fluorescence quenching method. The binding does not affect the oligomeric status of Ace. A cell viability assay of the antibacterial activity of Ace has been performed using various microbial strains. A homology model of Ace, consistent with the experimental results, has been constructed.
Collapse
Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India.
| | | | | | | | | | | |
Collapse
|
29
|
An BC, Lee SS, Wi SG, Bai HW, Lee SY, Chung BY. Improvement of chaperone activity of 2-Cys peroxiredoxin using gamma ray. JOURNAL OF RADIATION RESEARCH 2011; 52:694-700. [PMID: 22104267 DOI: 10.1269/jrr.11046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A typical 2-cysteine peroxiredoxin (2-Cys Prx) PaPrx can act alternatively as thioredoxin (Trx)-dependent peroxidase and molecular chaperone in Pseudomonas aeruginosa PAO1. In addition, the functional switch of PaPrx is regulated by its structural change which is dependently induced by stress conditions. In the present study, we examined the effect of gamma ray on structural modification related to chaperone activity of PaPrx. The structural change of PaPrx occupied with gamma ray irradiation (2 kGy) based on polyacrylamide gel electrophoresis (PAGE) analysis and the functional change also began. The enhanced chaperone activity was increased about 3-4 folds at 30 kGy gamma irradiation compared with nonirradiated PaPrx, while the peroxidase activity was significantly decreased. We also investigated the influence of the gamma ray on protein hydrophobicity as related to chaperone function. The exposure of hydrophobic domains reached a peak at 30 kGy gamma ray and then decreased dependently with increasing gamma irradiation. Our results suggest that highly enhanced chaperone activity could be adapted for use in bio-engineering systems and industrial applications such as enzyme stabilization during industrial process (inactivation protection), improvement of useful protein productivity (refolding and secretion) and industrial animal cell cultivation (stress protection).
Collapse
Affiliation(s)
- Byung Chull An
- Advanced Radiation Research Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | | | | | | | | | | |
Collapse
|
30
|
Chen Q, Yan M, Xiang F, Zhou X, Liu Y, Zheng F. Characterization of a mutant R11H αB-crystallin associated with human inherited cataract. Biol Chem 2010; 391:1391-400. [DOI: 10.1515/bc.2010.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
αB-Crystallin plays an important part in cataract development. A novel mutation (R11H) was previously detected by our group. In the present study, we set out to investigate the possible molecular mechanism by which the R11H mutation causes cataract. We found that the mutant αB-crystallin exhibits folding defects, decreased surface hydrophobicity and enhanced chaperone-like activity compared with the wild-type αB-crystallin. The mutant protein shows nearly the same molecular mass and thermal stability as the wild-type form. Transfection studies revealed that the R11H mutant was remarkably similar to the wild-type protein in its subcellular distribution, but has an abnormal ability to induce cell apoptosis. These results suggest that the changes in hydrophobic exposure and the abnormal ability to induce programmed cell death of the mutant protein are likely to be responsible for the onset of cataract.
Collapse
|
31
|
Krintel C, Mörgelin M, Logan DT, Holm C. Phosphorylation of hormone-sensitive lipase by protein kinase A in vitro promotes an increase in its hydrophobic surface area. FEBS J 2009; 276:4752-62. [PMID: 19664063 DOI: 10.1111/j.1742-4658.2009.07172.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hormone-sensitive lipase (EC 3.1.1.79; HSL) is a key enzyme in the mobilization of fatty acids from stored triacylglycerols. HSL activity is controlled by phosphorylation of at least four serines. In rat HSL, Ser563, Ser659 and Ser660 are phosphorylated by protein kinase A (PKA) in vitro as well as in vivo, and Ser660 and Ser659 have been shown to be the activity-controlling sites in vitro. The exact molecular events of PKA-mediated activation of HSL in vitro are yet to be determined, but increases in both Vmax and S0.5 seem to be involved, as recently shown for human HSL. In this study, the hydrophobic fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) was found to inhibit the hydrolysis of triolein by purified recombinant rat adipocyte HSL, with a decrease in the effect of bis-ANS upon PKA phosphorylation of HSL. The interaction of HSL with bis-ANS was found to have a Kd of 1 microM in binding assays. Upon PKA phosphorylation, the interactions of HSL with both bis-ANS and the alternative probe SYPRO Orange were increased. By negative stain transmission electron microscopy, phosphorylated HSL was found to have a closer interaction with phospholipid vesicles than unphosphorylated HSL. Taken together, our results show that HSL increases its hydrophobic nature upon phosphorylation by PKA. This suggests that PKA phosphorylation induces a conformational change that increases the exposed hydrophobic surface and thereby facilitates binding of HSL to the lipid substrate.
Collapse
Affiliation(s)
- Christian Krintel
- Department of Experimental Medical Science, Division of Diabetes, Metabolism and Endocrinology, Lund University, Sweden
| | | | | | | |
Collapse
|
32
|
Bose HS, Whittal RM, Bose M, Debnath D. Hydrophobic core of the steroidogenic acute regulatory protein for cholesterol transport. Biochemistry 2009; 48:1198-209. [PMID: 19170610 DOI: 10.1021/bi801514e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The steroidogenic acute regulatory protein (StAR), the first family member of START (StAR-related lipid transport) proteins, plays an essential role by facilitating the movement of cholesterol from the outer to inner mitochondrial membrane. Wild-type and mutant StAR binds cholesterol with similar intensity, but only wild-type StAR can transport it to mitochondria. Here, we report that the hydrophobic core is crucial for biological activity of proteins with START domains. Wild-type StAR increased steroidogenic activity by 7-9-fold compared to mutant R182L StAR, but both of them showed similar near-UV CD spectra. The fluorescence maximum of wild-type StAR is red shifted in comparison to mutant StAR under identical urea concentration. TFE increased the alpha-helical contribution of wild-type StAR more than the mutant protein. Acrylamide quenching for the wild-type protein (K(SV) = 12.0 +/- 0.2-11.2 +/- 0.5 M(-1)) exceeded that of the mutant protein (K(SV) = 4 +/- 0.2 M(-1)). Consistent with these findings, the hydrophobic probe ANS bound wild-type StAR (K(app) = 8.1 x 10(5) M(-1)) to a greater degree than mutant StAR (K(app) = 3.75 x 10(5) M(-1)). Partial proteolysis examined by mass spectrometry suggests that only wild-type StAR has a protease-sensitive C-terminus, but not the mutant. Stopped-flow CD revealed that the time of unfolding of mutant StAR was 0.017 s. In contrast, the wild-type StAR protein is unfolded in 16.3 s. In summary, these results demonstrate that wild-type StAR adopts a very flexible form due to the accommodation of more water molecules, while mutant StAR is generated by an alternate folding pathway making it inactive.
Collapse
Affiliation(s)
- Himangshu S Bose
- Department of Biomedical Sciences, Mercer University School of Medicine and Memorial Health University Medical Center, Savannah, Georgia 31404, USA.
| | | | | | | |
Collapse
|
33
|
Pleckaityte M, Mistinaite L, Mistiniene E, Dienys G, Zvirblis G. Biochemical properties of Hsp70 chaperone system fromMeiothermus ruber. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500175812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
34
|
Stawoska I, Wesełucha-Birczyńska A, Regonesi ME, Riva M, Tortora P, Stochel G. Interaction of selected divalent metal ions with human ataxin-3 Q36. J Biol Inorg Chem 2009; 14:1175-85. [DOI: 10.1007/s00775-009-0561-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022]
|
35
|
Fan DJ, Ding YW, Zhou JM. Structural rearrangements and the unfolding mechanism of a Trigger Factor mutant studied by multiple structural probes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:944-52. [DOI: 10.1016/j.bbapap.2009.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 03/10/2009] [Accepted: 03/16/2009] [Indexed: 10/21/2022]
|
36
|
Cong WT, Hwang SY, Jin LT, Choi JK. Improved conditions for fluorescent staining of proteins with 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid in SDS-PAGE. Electrophoresis 2009; 29:4487-94. [PMID: 19035403 DOI: 10.1002/elps.200800124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A simple and sensitive fluorescent staining method for the detection of proteins in SDS-PAGE, namely IB (improved 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid) stain, is described. Non-covalent hydrophobic probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non-specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.
Collapse
Affiliation(s)
- Wei-Tao Cong
- College of Pharmacy & Research Institute of Drug Development, Chonnam National University, Gwangju, South Korea
| | | | | | | |
Collapse
|
37
|
Wolff J. Plasma membrane tubulin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1415-33. [PMID: 19328773 DOI: 10.1016/j.bbamem.2009.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/13/2009] [Accepted: 03/19/2009] [Indexed: 01/17/2023]
Abstract
The association of tubulin with the plasma membrane comprises multiple levels of penetration into the bilayer: from integral membrane protein, to attachment via palmitoylation, to surface binding, and to microtubules attached by linker proteins to proteins in the membrane. Here we discuss the soundness and weaknesses of the chemical and biochemical evidence marshaled to support these associations, as well as the mechanisms by which tubulin or microtubules may regulate functions at the plasma membrane.
Collapse
Affiliation(s)
- J Wolff
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
38
|
Bañares-Hidalgo A, Bolaños-Gutiérrez A, Gil F, Cabré EJ, Pérez-Gil J, Estrada P. Self-aggregation of a recombinant form of the propeptide NH2-terminal of the precursor of pulmonary surfactant protein SP-B: a conformational study. J Ind Microbiol Biotechnol 2008; 35:1367-76. [PMID: 18797948 DOI: 10.1007/s10295-008-0437-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 07/30/2008] [Indexed: 12/23/2022]
Abstract
A recombinant form of the peptide N-terminally positioned from proSP-B (SP-BN) has been produced in Escherichia coli as fusion with the Maltose Binding Protein, separated from it by Factor Xa cleavage and purified thereafter. This protein module is thought to control assembly of mature SP-B, a protein essential for respiration, in pulmonary surfactant as it progress through the progressively acidified secretory pathway of pneumocytes. Self-aggregation studies of the recombinant propeptide have been carried out as the pH of the medium evolved from neutral to moderately acid, again to neutral and finally basic. The profile of aggregation versus subsequent changes in pH showed differences depending on the ionic strength of the medium, low or moderate, and the presence of additives such as L-arginine (a known aggregation suppressor) and Ficoll 70 (a macromolecular crowder). Circular dichroism studies of SP-BN samples along the aggregation process showed a decrease in alpha-helical content and a concomitant increase in beta-sheet. Intrinsic fluorescence emission of SP-BN was dominated by the emission of Trp residues in neutral medium, being its emission maximum shifted to red at low pH, suggesting that the protein undergoes a pH-dependent conformational change that increases the exposure of their Trp to the environment. A marked increase in the fluorescence emission of the extrinsic probe bis-ANS indicated the exposure of hydrophobic regions of SP-BN at pH 5. The fluorescence of bis-ANS decreased slightly at low ionic strength, but to a great extent at moderate ionic strength when the pH was reversed to neutrality, suggesting that self-aggregation properties of the SP-BN module could be tightly modulated by the conditions of pH and the ionic environment encountered by pulmonary surfactant during assembly and secretion.
Collapse
Affiliation(s)
- A Bañares-Hidalgo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Biología, Universidad Complutense, Ciudad Universitaria, 28040, Madrid, Spain
| | | | | | | | | | | |
Collapse
|
39
|
Biochemical and structural characterisation of cutinase mutants in the presence of the anionic surfactant AOT. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1326-34. [DOI: 10.1016/j.bbapap.2008.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 04/08/2008] [Accepted: 04/22/2008] [Indexed: 11/18/2022]
|
40
|
Raab R, Swietnicki W. Yersinia pestis YopD 150–287 fragment is partially unfolded in the native state. Protein Expr Purif 2008; 58:53-60. [DOI: 10.1016/j.pep.2007.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 10/30/2007] [Accepted: 11/03/2007] [Indexed: 01/25/2023]
|
41
|
Shi Y, Fan DJ, Li SX, Zhang HJ, Perrett S, Zhou JM. Identification of a potential hydrophobic peptide binding site in the C-terminal arm of trigger factor. Protein Sci 2007; 16:1165-75. [PMID: 17525465 PMCID: PMC2206664 DOI: 10.1110/ps.062623707] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Trigger factor (TF) is the first chaperone to interact with nascent chains and facilitate their folding in bacteria. Escherichia coli TF is 432 residues in length and contains three domains with distinct structural and functional properties. The N-terminal domain of TF is important for ribosome binding, and the M-domain carries the PPIase activity. However, the function of the C-terminal domain remains unclear, and the residues or regions directly involved in substrate binding have not yet been identified. Here, a hydrophobic probe, bis-ANS, was used to characterize potential substrate-binding regions. Results showed that bis-ANS binds TF with a 1:1 stoichiometry and a K(d) of 16 microM, and it can be covalently incorporated into TF by UV-light irradiation. A single bis-ANS-labeled peptide was obtained by tryptic digestion and identified by MALDI-TOF mass spectrometry as Asn391-Lys392. In silico docking analysis identified a single potential binding site for bis-ANS on the TF molecule, which is adjacent to this dipeptide and lies in the pocket formed by the C-terminal arms. The bis-ANS-labeled TF completely lost the ability to assist GAPDH or lysozyme refolding and showed increased protection toward cleavage by alpha-chymotrypsin, suggesting blocking of hydrophobic residues. The C-terminal truncation mutant TF389 also showed no chaperone activity and could not bind bis-ANS. These results suggest that bis-ANS binding may mimic binding of a substrate peptide and that the C-terminal region of TF plays an important role in hydrophobic binding and chaperone function.
Collapse
Affiliation(s)
- Yi Shi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | |
Collapse
|
42
|
Mocan I, Georgescauld F, Gonin P, Thoraval D, Cervoni L, Giartosio A, Dabernat-Arnaud S, Crouzet M, Lacombe ML, Lascu I. Protein phosphorylation corrects the folding defect of the neuroblastoma (S120G) mutant of human nucleoside diphosphate kinase A/Nm23-H1. Biochem J 2007; 403:149-56. [PMID: 17155928 PMCID: PMC1828887 DOI: 10.1042/bj20061141] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Human nucleoside diphosphate (NDP) kinase A is a 'house-keeping' enzyme essential for the synthesis of nonadenine nucleoside (and deoxynucleoside) 5'-triphosphate. It is involved in complex cellular regulatory functions including the control of metastatic tumour dissemination. The mutation S120G has been identified in high-grade neuroblastomas. We have shown previously that this mutant has a folding defect: the urea-denatured protein could not refold in vitro. A molten globule folding intermediate accumulated, whereas the wild-type protein folded and associated into active hexamers. In the present study, we report that autophosphorylation of the protein corrected the folding defect. The phosphorylated S120G mutant NDP kinase, either autophosphorylated with ATP as donor, or chemically prosphorylated by phosphoramidate, refolded and associated quickly with high yield. Nucleotide binding had only a small effect. ADP and the non-hydrolysable ATP analogue 5'-adenyly-limido-diphosphate did not promote refolding. ATP-promoted refolding was strongly inhibited by ADP, indicating protein dephosphorylation. Our findings explain why the mutant enzyme is produced in mammalian cells and in Escherichia coli in a soluble form and is active, despite the folding defect of the S120G mutant observed in vitro. We generated an inactive mutant kinase by replacing the essential active-site histidine residue at position 118 with an asparagine residue, which abrogates the autophosphorylation. The double mutant H118N/S120G was expressed in inclusion bodies in E. coli. Its renaturation stops at a folding intermediate and cannot be reactivated by ATP in vitro. The transfection of cells with this double mutant might be a good model to study the cellular effects of folding intermediates.
Collapse
Affiliation(s)
- Iulia Mocan
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
| | - Florian Georgescauld
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
| | - Philippe Gonin
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
| | - Didier Thoraval
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
| | - Laura Cervoni
- †Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’ and the Center of Molecular Biology of Consiglio Nazionale delle Ricerche, Università degli Studi ‘La Sapienza’, 00185 Rome, Italy
| | - Anna Giartosio
- †Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’ and the Center of Molecular Biology of Consiglio Nazionale delle Ricerche, Università degli Studi ‘La Sapienza’, 00185 Rome, Italy
| | | | - Marc Crouzet
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
| | - Marie-Lise Lacombe
- §Unité 680 INSERM, Faculté de Médecine Pierre et Marie Curie, site Saint-Antoine, 75012 Paris, France
| | - Ioan Lascu
- *Institut de Biochimie et Génétique Cellulaires (UMR 5095), Université Victor Segalen Bordeaux2 and CNRS, 33077 Bordeaux Cedex, France
- To whom correspondence should be addressed (email )
| |
Collapse
|
43
|
Samaddar S, Mandal AK, Mondal SK, Sahu K, Bhattacharyya K, Roy S. Solvation Dynamics of a Protein in the Pre Molten Globule State. J Phys Chem B 2006; 110:21210-5. [PMID: 17048947 DOI: 10.1021/jp064136g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.
Collapse
Affiliation(s)
- Soma Samaddar
- Department of Biophysics, Bose Institute, P 1/12 CIT, Scheme VIIM, Kolkata 700 054, India
| | | | | | | | | | | |
Collapse
|
44
|
Affiliation(s)
- Heinrich Roder
- Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA.
| | | | | |
Collapse
|
45
|
Sheets DW, Okamoto T, Dijkgraaf LC, Milam SB, Schmitz JP, Zardeneta G. Free Radical Damage in Facsimile Synovium: Correlation with Adhesion Formation in Osteoarthritic TMJs. J Prosthodont 2006; 15:9-19. [PMID: 16433646 DOI: 10.1111/j.1532-849x.2006.00063.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE The purpose of this study was to use the rat air pouch model of facsimile synovium to evaluate oxidative stress as a primary mechanism in the pathogenesis of degenerative temporomandibular joint (TMJ) disease. MATERIALS AND METHODS Forty-nine Sprague-Dawley adult female rats were used to generate the standard rat air pouch model of facsimile synovium. This was accomplished by daily air injections (20 cc) subdermally through the dorsal skin. Hydrogen peroxide and ferrous iron (components of the Fenton reaction which generate free radicals) were introduced into the pouches of the 4-, 7-, and 14-day groups to generate oxidative stress. Control rats were injected with phosphate-buffered solution (PBS), pH 7.4. Either N-acetylcysteine (NAC), a powerful free radical scavenger, or ibuprofen were simultaneously injected with the Fenton reagents into the pouches of the 14-day treatment groups to modulate free radical-mediated protein damage to the synovium. Animals were euthanized at appropriate experimental intervals and biopsies obtained from specimens to analyze: (1) proteins' amino acid modification (carbonyl group formation), (2) protein hydrophobicity, (3) detection of low molecular weight protein degradation products, and (4) histological and gross anatomical observations. RESULTS Free radicals introduced into the rat air pouch interacted with synovial tissues causing oxidation and breakdown of proteins. Clinical evidence of adhesion formation consistent with features found in osteoarthritis of the TMJ developed. The groups subjected to oxidative stress experienced statistically significant (p < 0.05) increases in carbonyl formation, carbonyls/protein, and low molecular weight protein fragments. These groups also showed significant (p < 0.05) hydrophobicity changes consistent with free radical attack. Control synovial tissues were statistically undamaged. The 14-day NAC and ibuprofen treatment groups experienced statistically significant (p < 0.05) decreases in total carbonyl formation, carbonyls/protein, and hydrophobicity. Histological and gross observations in free radical damaged synovium exhibited features consistent with known arthoscopic and arthrocentesis findings in diseased TMJs. CONCLUSIONS This study suggests that the rat air pouch model of facsimile synovium develops clinical evidence of adhesions and biochemical signs of protein modification when subjected to free radical attack. NAC and ibuprofen prevented carbonyl formation as well as hydrophobicity changes indicative of oxidative stress damage in facsimile synovium. These findings are consistent with features of degenerative human TMJ disease. Future direction may be taken from this study to postulate new analysis techniques and treatment modalities for patients with degenerative TMJ disease.
Collapse
Affiliation(s)
- Donald W Sheets
- Department of Prosthodontics, Wilford Hall Medical Center, Lackland AFB, San Antonio, TX, USA
| | | | | | | | | | | |
Collapse
|
46
|
Jang HH, Kim SY, Park SK, Jeon HS, Lee YM, Jung JH, Lee SY, Chae HB, Jung YJ, Lee KO, Lim CO, Chung WS, Bahk JD, Yun DJ, Cho MJ, Lee SY. Phosphorylation and concomitant structural changes in human 2-Cys peroxiredoxin isotype I differentially regulate its peroxidase and molecular chaperone functions. FEBS Lett 2005; 580:351-5. [PMID: 16376335 DOI: 10.1016/j.febslet.2005.12.030] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Accepted: 12/08/2005] [Indexed: 10/25/2022]
Abstract
The H2O2-catabolizing peroxidase activity of human peroxiredoxin I (hPrxI) was previously shown to be regulated by phosphorylation of Thr90. Here, we show that hPrxI forms multiple oligomers with distinct secondary structures. HPrxI is a dual function protein, since it can behave either as a peroxidase or as a molecular chaperone. The effects of phosphorylation of hPrxI on its protein structure and dual functions were determined using site-directed mutagenesis, in which the phosphorylation site was substituted with aspartate to mimic the phosphorylated status of the protein (T90D-hPrxI). Phosphorylation of the protein induces significant changes in its protein structure from low molecular weight (MW) protein species to high MW protein complexes as well as its dual functions. In contrast to the wild type (WT)- and T90A-hPrxI, the T90D-hPrxI exhibited a markedly reduced peroxidase activity, but showed about sixfold higher chaperone activity than WT-hPrxI.
Collapse
Affiliation(s)
- Ho Hee Jang
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Zhang L, Lookene A, Wu G, Olivecrona G. Calcium triggers folding of lipoprotein lipase into active dimers. J Biol Chem 2005; 280:42580-91. [PMID: 16179346 DOI: 10.1074/jbc.m507252200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active form of lipoprotein lipase (LPL) is a noncovalent homodimer of 55-kDa subunits. The dimer is unstable and tends to undergo irreversible dissociation into inactive monomers. We noted that a preparation of such monomers slowly regained traces of activity under assay conditions with substrate, heparin, and serum or in cell culture medium containing serum. We therefore studied the refolding pathway of LPL after full denaturation in 6 M guanidinium chloride or after dissociation into monomers in 1 M guanidinium chloride. In crude systems, we identified serum as the factor promoting reactivation. Further investigations demonstrated that Ca2+ was the crucial component in serum for reactivation of LPL and that refolding involved at least two steps. Studies of far-UV circular dichroism, fluorescence, and proteolytic cleavage patterns showed that LPL started to refold from the C-terminal domain, independent of calcium. The first step was rapid and resulted in formation of an inactive monomer with a completely folded C-terminal domain, whereas the N-terminal domain was in the molten globule state. The second step was promoted by Ca2+ and converted LPL monomers from the molten globule state to dimerization-competent and more tightly folded monomers that rapidly formed active LPL dimers. The second step was slow, and it appears that proline isomerization (rather than dimerization as such) is rate-limiting. Inactive monomers isolated from human tissue recovered activity under the influence of Ca2+. We speculate that Ca2+-dependent control of LPL dimerization might be involved in the normal post-translational regulation of LPL activity.
Collapse
Affiliation(s)
- Liyan Zhang
- Department of Medical Biosciences, Physiological Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | | |
Collapse
|
48
|
Celej MS, Dassie SA, Freire E, Bianconi ML, Fidelio GD. Ligand-induced thermostability in proteins: thermodynamic analysis of ANS-albumin interaction. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1750:122-33. [PMID: 15972267 DOI: 10.1016/j.bbapap.2005.05.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 05/03/2005] [Accepted: 05/03/2005] [Indexed: 10/25/2022]
Abstract
A comparative thermodynamic study of the interaction of anilinonaphthalene sulfonate (ANS) derivatives with bovine serum albumin (BSA) was performed by using differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). The chemically related ligands, 1,8-ANS and 2,6-ANS, present a similar affinity for BSA with different binding energetics. The analysis of the binding driving forces suggests that not only hydrophobic effect but also electrostatic interactions are relevant, even though they have been extensively used as probes for non-polar domains in proteins. Ligand association leads to an increase in protein thermostability, indicating that both dyes interact mainly with native BSA. ITC data show that 1,8-ANS and 2,6-ANS have a moderate affinity for BSA, with an association constant of around 1-9x10(5) M(-1) for the high-affinity site. Ligand binding is disfavoured by conformational entropy. The theoretical model used to simulate DSC data satisfactorily reproduces experimental thermograms, validating this approach as one which provides new insights into the interaction between one or more ligands with a protein. By comparison with 1,8-ANS, 2,6-ANS appears as a more "inert" probe to assess processes which involve conformational changes in proteins.
Collapse
Affiliation(s)
- M Soledad Celej
- Departamento de Química Biológica-CIQUIBIC, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, 5000, Córdoba, Argentina
| | | | | | | | | |
Collapse
|
49
|
Kimura T, Akiyama S, Uzawa T, Ishimori K, Morishima I, Fujisawa T, Takahashi S. Specifically collapsed intermediate in the early stage of the folding of ribonuclease A. J Mol Biol 2005; 350:349-62. [PMID: 15935376 DOI: 10.1016/j.jmb.2005.04.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2005] [Revised: 04/28/2005] [Accepted: 04/29/2005] [Indexed: 11/21/2022]
Abstract
Nature of the burst-phase signals of protein folding has been the subject of much debate as to whether the signals represent the formation of early intermediates or the non-specific collapse of unfolded polypeptides. To distinguish the two possibilities, the submillisecond folding dynamics of ribonuclease A (RNase A) was examined, and compared with those of the disulfide bond-ruptured analog of RNase A (r-RNase A). The circular dichroism measurements on RNase A showed the burst-phase signal within 320 micros after the initiation of the folding reaction, which was identical to that observed for r-RNase A. In contrast, the burst phase increase in the extrinsic fluorescence from 1-anilino-8-naphthalene sulfonate (ANS) was observed for RNase A but not for r-RNase A. The kinetic titration experiment of the ANS fluorescence intensity showed the presence of a specific binding site for ANS in the fast-refolding component of RNase A. The small-angle X-ray scattering measurements at approximately 22 ms after initiating the folding reaction demonstrated that the burst phase conformations of the medium and slow-refolding components of RNase A were distinctly smaller than that of r-RNase A. These results indicated the difference in the burst phase conformations of RNase A and r-RNase A. Since r-RNase A is denatured in the physiological solution condition, the burst-phase signal of RNase A was interpreted as the formation of the folding intermediate with specific conformations.
Collapse
Affiliation(s)
- Tetsunari Kimura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | | | | | | | | | | | | |
Collapse
|
50
|
Krantz BA, Trivedi AD, Cunningham K, Christensen KA, Collier RJ. Acid-induced unfolding of the amino-terminal domains of the lethal and edema factors of anthrax toxin. J Mol Biol 2005; 344:739-56. [PMID: 15533442 DOI: 10.1016/j.jmb.2004.09.067] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 09/22/2004] [Accepted: 09/23/2004] [Indexed: 11/22/2022]
Abstract
The two enzymatic components of anthrax toxin, lethal factor (LF) and edema factor (EF), are transported to the cytosol of mammalian cells by the third component, protective antigen (PA). A heptameric form of PA binds LF and/or EF and, under the acidic conditions encountered in endosomes, generates a membrane-spanning pore that is thought to serve as a passageway for these enzymes to enter the cytosol. The pore contains a 14-stranded transmembrane beta-barrel that is too narrow to accommodate a fully folded protein, necessitating that LF and EF unfold, at least partly, in order to pass. Here, we describe the pH-dependence of the unfolding of LF(N) and EF(N), the 30kDa N-terminal PA-binding domains, and minimal translocatable units, of LF and EF. Equilibrium chemical denaturation studies using fluorescence and circular dichroism spectroscopy show that each protein unfolds via a four-state mechanism: N<-->I<-->J<-->U. The acid-induced N-->I transition occurs within the pH range of the endosome (pH 5-6). The I state predominates at lower pH values, and the J and U states are populated significantly only in the presence of denaturant. The I state is compact and has characteristics of a molten globule, as shown by its retention of significant secondary structure and its ability to bind an apolar fluorophore. The N-->I transition leads to an overall 60% increase in buried surface area exposure. The J state is expanded significantly and has diminished secondary structure content. We analyze the different protonation states of LF(N) and EF(N) in terms of a linked equilibrium proton binding model and discuss the implications of our findings for the mechanism of acidic pH-induced translocation of anthrax toxin. Finally, analysis of the structure of the transmembrane beta-barrel of PA shows that it can accommodate alpha-helix, and we suggest that the steric constraints and composition of the lumen may promote alpha-helix formation.
Collapse
Affiliation(s)
- Bryan A Krantz
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
| | | | | | | | | |
Collapse
|