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Beygmoradi A, Homaei A, Hemmati R, Fernandes P. Recombinant protein expression: Challenges in production and folding related matters. Int J Biol Macromol 2023; 233:123407. [PMID: 36708896 DOI: 10.1016/j.ijbiomac.2023.123407] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Protein folding is a biophysical process by which proteins reach a specific three-dimensional structure. The amino acid sequence of a polypeptide chain contains all the information needed to determine the final three-dimensional structure of a protein. When producing a recombinant protein, several problems can occur, including proteolysis, incorrect folding, formation of inclusion bodies, or protein aggregation, whereby the protein loses its natural structure. To overcome such limitations, several strategies have been developed to address each specific issue. Identification of proper protein refolding conditions can be challenging, and to tackle this high throughput screening for different recombinant protein folding conditions can prove a sound solution. Different approaches have emerged to tackle refolding issues. One particular approach to address folding issues involves molecular chaperones, highly conserved proteins that contribute to proper folding by shielding folding proteins from other proteins that could hinder the process. Proper protein folding is one of the main prerequisites for post-translational modifications. Incorrect folding, if not dealt with, can lead to a buildup of protein misfoldings that damage cells and cause widespread abnormalities. Said post-translational modifications, widespread in eukaryotes, are critical for protein structure, function and biological activity. Incorrect post-translational protein modifications may lead to individual consequences or aggregation of therapeutic proteins. In this review article, we have tried to examine some key aspects of recombinant protein expression. Accordingly, the relevance of these proteins is highlighted, major problems related to the production of recombinant protein and to refolding issues are pinpointed and suggested solutions are presented. An overview of post-translational modification, their biological significance and methods of identification are also provided. Overall, the work is expected to illustrate challenges in recombinant protein expression.
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Affiliation(s)
- Azadeh Beygmoradi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
| | - Roohullah Hemmati
- Department of Biology, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Pedro Fernandes
- DREAMS and Faculdade de Engenharia, Universidade Lusófona de Humanidades e Tecnologias, Av. Campo Grande 376, 1749-024 Lisboa, Portugal; iBB-Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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2
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Verma N, Dollinger P, Kovacic F, Jaeger KE, Gohlke H. The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J Comput Chem 2019; 41:500-512. [PMID: 31618459 DOI: 10.1002/jcc.26085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
Lipases are essential and widely used biocatalysts. Hence, the production of lipases requires a detailed understanding of the molecular mechanism of its folding and secretion. Lipase A from Pseudomonas aeruginosa, PaLipA, constitutes a prominent example that has additional relevance because of its role as a virulence factor in many diseases. PaLipA requires the assistance of a membrane-integrated steric chaperone, the lipase-specific foldase Lif, to achieve its enzymatically active state. However, the molecular mechanism of how Lif activates its cognate lipase has remained elusive. Here, we show by molecular dynamics simulations at the atomistic level and potential of mean force computations that Lif catalyzes the activation process of PaLipA by structurally stabilizing an intermediate PaLipA conformation, particularly a β-sheet in the region of residues 17-30, such that the opening of PaLipA's lid domain is facilitated. This opening allows substrate access to PaLipA's catalytic site. A surprising and so far not fully understood aspect of our study is that the open state of PaLipA is unstable compared to the closed one according to our computational and in vitro biochemical results. We thus speculate that further interactions of PaLipA with the Xcp secretion machinery and/or components of the extracellular matrix contribute to the remaining activity of secreted PaLipA. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Neha Verma
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Peter Dollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
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3
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Negron C, Pearlman DA, del Angel G. Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA. PLoS One 2019; 14:e0214015. [PMID: 30889230 PMCID: PMC6424398 DOI: 10.1371/journal.pone.0214015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Missense mutations can have disastrous effects on the function of a protein. And as a result, they have been implicated in numerous diseases. However, the majority of missense variants only have a nominal impact on protein function. Thus, the ability to distinguish these two classes of missense mutations would greatly aid drug discovery efforts in target identification and validation as well as medical diagnosis. Monitoring the co-occurrence of a given missense mutation and a disease phenotype provides a pathway for classifying functionally disrupting missense mutations. But, the occurrence of a specific missense variant is often extremely rare making statistical links challenging to infer. In this study, we benchmark a physics-based approach for predicting changes in stability, MM-GBSA, and apply it to classifying mutations as functionally disrupting. A large and diverse dataset of 990 residue mutations in beta-lactamase TEM1 is used to assess performance as it is rich in both functionally disrupting mutations and functionally neutral/beneficial mutations. On this dataset, we compare the performance of MM-GBSA to alternative strategies for predicting functionally disrupting mutations. We observe that the MM-GBSA method obtains an area under the curve (AUC) of 0.75 on the entire dataset, outperforming all other predictors tested. More importantly, MM-GBSA’s performance is robust to various divisions of the dataset, speaking to the generality of the approach. Though there is one notable exception: Mutations on the surface of the protein are the mutations that are the most difficult to classify as functionally disrupting for all methods tested. This is likely due to the many mechanisms available to surface mutations to disrupt function, and thus provides a direction of focus for future studies.
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Affiliation(s)
| | | | - Guillermo del Angel
- Alexion Pharmaceuticals Inc., Boston, Massachusetts, United States of America
- * E-mail:
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4
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Abstract
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo. REVIEWERS This article was reviewed by Eugene Koonin and Frank Eisenhaber.
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5
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Ciechanover A, Kwon YT. Protein Quality Control by Molecular Chaperones in Neurodegeneration. Front Neurosci 2017; 11:185. [PMID: 28428740 PMCID: PMC5382173 DOI: 10.3389/fnins.2017.00185] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis (proteostasis) requires the timely degradation of misfolded proteins and their aggregates by protein quality control (PQC), of which molecular chaperones are an essential component. Compared with other cell types, PQC in neurons is particularly challenging because they have a unique cellular structure with long extensions. Making it worse, neurons are postmitotic, i.e., cannot dilute toxic substances by division, and, thus, are highly sensitive to misfolded proteins, especially as they age. Failure in PQC is often associated with neurodegenerative diseases, such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), and prion disease. In fact, many neurodegenerative diseases are considered to be protein misfolding disorders. To prevent the accumulation of disease-causing aggregates, neurons utilize a repertoire of chaperones that recognize misfolded proteins through exposed hydrophobic surfaces and assist their refolding. If such an effort fails, chaperones can facilitate the degradation of terminally misfolded proteins through either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). If soluble, the substrates associated with chaperones, such as Hsp70, are ubiquitinated by Ub ligases and degraded through the proteasome complex. Some misfolded proteins carrying the KFERQ motif are recognized by the chaperone Hsc70 and delivered to the lysosomal lumen through a process called, chaperone-mediated autophagy (CMA). Aggregation-prone misfolded proteins that remain unprocessed are directed to macroautophagy in which cargoes are collected by adaptors, such as p62/SQSTM-1/Sequestosome-1, and delivered to the autophagosome for lysosomal degradation. The aggregates that have survived all these refolding/degradative processes can still be directly dissolved, i.e., disaggregated by chaperones. Studies have shown that molecular chaperones alleviate the pathogenic symptoms by neurodegeneration-causing protein aggregates. Chaperone-inducing drugs and anti-aggregation drugs are actively exploited for beneficial effects on symptoms of disease. Here, we discuss how chaperones protect misfolded proteins from aggregation and mediate the degradation of terminally misfolded proteins in collaboration with cellular degradative machinery. The topics also include therapeutic approaches to improve the expression and turnover of molecular chaperones and to develop anti-aggregation drugs.
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Affiliation(s)
- Aaron Ciechanover
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Technion Integrated Cancer Center, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National UniversitySeoul, South Korea
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6
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Tsuchiya Y, Noguchi T, Yoshihara D, Roy B, Yamamoto T, Shinkai S. Conformation Control of a Conjugated Polymer through Complexation with Bile Acids Generates Its Novel Spectral and Morphological Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12403-12412. [PMID: 27327101 DOI: 10.1021/acs.langmuir.6b01639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Control of higher-order polymer structures attracts a great deal of interest for many researchers when they lead to the development of materials having various advanced functions. Among them, conjugated polymers that are useful as starting materials in the design of molecular wires are particularly attractive. However, an equilibrium existing between isolated chains and bundled aggregates is inevitable and has made their physical properties very complicated. As an attempt to simplify this situation, we previously reported that a polymer chain of a water-soluble polythiophene could be isolated through complexation with a helix-forming polysaccharide. More recently, a covalently self-threading polythiophene was reported, the main chain of which was physically protected from self-folding and chain-chain π-stacking. In this report, we wish to report a new strategy to isolate a water-soluble polythiophene and to control its higher-order structure by a supramolecular approach: that is, among a few bile acids, lithocholate can form stoichiometric complexes with cationic polythiophene to isolate the polymer chain, and the higher-order structure is changeable by the molar ratio. The optical and morphological studies have been thoroughly performed, and the resultant complex has been applied to the selective recognition of two AMP structural isomers.
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Affiliation(s)
- Youichi Tsuchiya
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), Fukuoka Industry-Academia Symphonicity (FiaS), Kyudaishinmachi 4-1, Nishi-ku, Fukuoka 819-0388, Japan
| | | | - Daisuke Yoshihara
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), Fukuoka Industry-Academia Symphonicity (FiaS), Kyudaishinmachi 4-1, Nishi-ku, Fukuoka 819-0388, Japan
| | | | - Tatsuhiro Yamamoto
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), Fukuoka Industry-Academia Symphonicity (FiaS), Kyudaishinmachi 4-1, Nishi-ku, Fukuoka 819-0388, Japan
| | - Seiji Shinkai
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), Fukuoka Industry-Academia Symphonicity (FiaS), Kyudaishinmachi 4-1, Nishi-ku, Fukuoka 819-0388, Japan
- Department of Nanoscience, Faculty of Engineering, Sojo University , Ikeda 4-22-1, Nishi-ku, Kumamoto 860-0082, Japan
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7
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Freeman MF, Helf MJ, Bhushan A, Morinaka BI, Piel J. Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium. Nat Chem 2016; 9:387-395. [DOI: 10.1038/nchem.2666] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/02/2016] [Indexed: 12/20/2022]
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8
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Abstract
Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC)
- Brussels
- Belgium
- Vrije Universiteit Brussel
- Brussels
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9
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Foldase and inhibitor functionalities of the pepsinogen prosegment are encoded within discrete segments of the 44 residue domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1300-6. [PMID: 26003941 DOI: 10.1016/j.bbapap.2015.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/22/2022]
Abstract
Pepsin is initially produced as the zymogen pepsinogen, containing a 44 residue prosegment (PS) domain. When folded without the PS, pepsin forms a thermodynamically stable denatured state (refolded pepsin, Rp). To guide native folding, the PS binds to Rp, stabilizes the folding transition state, and binds tightly to native pepsin (Np), thereby driving the folding equilibrium to favor the native state. It is unknown whether these functionalities of the PS are encoded within the entire sequence or within discrete segments. PS residues 1p-29p correspond to a highly conserved region in pepsin-like aspartic proteases and we hypothesized that this segment is critical to PS-catalyzed folding. This notion was tested in the present study by characterizing the ability of various truncated PS peptides to bind Rp, catalyze folding from Rp to Np, and to inhibit Np. Four PS truncations were examined, corresponding to PS residues 1p-16p (PS1-16), 1p-29p (PS1-29), 17p-44p (PS17-44) and 30p-44p (PS30-44). The three PS functionalities could be ascribed primarily to discrete regions within the highly conserved motif: 1p-16p dictated Rp binding, 17p-29p dictated Np binding/inhibition, while the entire 1p-29p dictated transition state binding/catalyzing folding. Conversely, PS30-44 played no obvious role in PS-catalyzed folding; it is hypothesized that this more variable region may serve as a linker between PS1-29 and the mature domain. The high sequence conservation of PS1-29 and its role in catalyzing pepsin folding strongly suggest that there is a conserved PS-catalyzed folding mechanism shared by pepsin-like aspartic proteases with this motif.
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10
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Kobayashi H, Yoshida T, Miyakawa T, Tashiro M, Okamoto K, Yamanaka H, Tanokura M, Tsuge H. Structural Basis for Action of the External Chaperone for a Propeptide-deficient Serine Protease from Aeromonas sobria. J Biol Chem 2015; 290:11130-43. [PMID: 25784551 DOI: 10.1074/jbc.m114.622852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 11/06/2022] Open
Abstract
Subtilisin-like proteases are broadly expressed in organisms ranging from bacteria to mammals. During maturation of these enzymes, N-terminal propeptides function as intramolecular chaperones, assisting the folding of their catalytic domains. However, we have identified an exceptional case, the serine protease from Aeromonas sobria (ASP), that lacks a propeptide. Instead, ORF2, a protein encoded just downstream of asp, appears essential for proper ASP folding. The mechanism by which ORF2 functions remains an open question, because it shares no sequence homology with any known intramolecular propeptide or other protein. Here we report the crystal structure of the ORF2-ASP complex and the solution structure of free ORF2. ORF2 consists of three regions: an N-terminal extension, a central body, and a C-terminal tail. Together, the structure of the central body and the C-terminal tail is similar to that of the intramolecular propeptide. The N-terminal extension, which is not seen in other subtilisin-like enzymes, is intrinsically disordered but forms some degree of secondary structure upon binding ASP. We also show that C-terminal (ΔC1 and ΔC5) or N-terminal (ΔN43 and ΔN64) deletion eliminates the ability of ORF2 to function as a chaperone. Characterization of the maturation of ASP with ORF2 showed that folding occurs in the periplasmic space and is followed by translocation into extracellular space and dissociation from ORF2, generating active ASP. Finally, a PSI-BLAST search revealed that operons encoding subtilases and their external chaperones are widely distributed among Gram-negative bacteria, suggesting that ASP and its homologs form a novel family of subtilases having an external chaperone.
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Affiliation(s)
- Hidetomo Kobayashi
- From the Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan
| | - Toru Yoshida
- the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Takuya Miyakawa
- the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mitsuru Tashiro
- the Department of Chemistry, College of Science and Technology, Meisei University, Hodokubo, Hino, Tokyo 191-0042, Japan, and
| | - Keinosuke Okamoto
- the Department of Pharmacogenetics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hiroyasu Yamanaka
- From the Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan
| | - Masaru Tanokura
- the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideaki Tsuge
- the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan,
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11
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Molecular chaperone dysfunction in neurodegenerative diseases and effects of curcumin. BIOMED RESEARCH INTERNATIONAL 2014; 2014:495091. [PMID: 25386560 PMCID: PMC4217372 DOI: 10.1155/2014/495091] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/23/2014] [Indexed: 01/26/2023]
Abstract
The intra- and extracellular accumulation of misfolded and aggregated amyloid proteins is a common feature in several neurodegenerative diseases, which is thought to play a major role in disease severity and progression. The principal machineries maintaining proteostasis are the ubiquitin proteasomal and lysosomal autophagy systems, where heat shock proteins play a crucial role. Many protein aggregates are degraded by the lysosomes, depending on aggregate size, peptide sequence, and degree of misfolding, while others are selectively tagged for removal by heat shock proteins and degraded by either the proteasome or phagosomes. These systems are compromised in different neurodegenerative diseases. Therefore, developing novel targets and classes of therapeutic drugs, which can reduce aggregates and maintain proteostasis in the brains of neurodegenerative models, is vital. Natural products that can modulate heat shock proteins/proteosomal pathway are considered promising for treating neurodegenerative diseases. Here we discuss the current knowledge on the role of HSPs in protein misfolding diseases and knowledge gained from animal models of Alzheimer's disease, tauopathies, and Huntington's diseases. Further, we discuss the emerging treatment regimens for these diseases using natural products, like curcumin, which can augment expression or function of heat shock proteins in the cell.
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12
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Dee DR, Horimoto Y, Yada RY. Conserved prosegment residues stabilize a late-stage folding transition state of pepsin independently of ground states. PLoS One 2014; 9:e101339. [PMID: 24983988 PMCID: PMC4077824 DOI: 10.1371/journal.pone.0101339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 06/05/2014] [Indexed: 11/24/2022] Open
Abstract
The native folding of certain zymogen-derived enzymes is completely dependent upon a prosegment domain to stabilize the folding transition state, thereby catalyzing the folding reaction. Generally little is known about how the prosegment accomplishes this task. It was previously shown that the prosegment catalyzes a late-stage folding transition between a stable misfolded state and the native state of pepsin. In this study, the contributions of specific prosegment residues to catalyzing pepsin folding were investigated by introducing individual Ala substitutions and measuring the effects on the bimolecular folding reaction between the prosegment peptide and pepsin. The effects of mutations on the free energies of the individual misfolded and native ground states and the transition state were compared using measurements of prosegment-pepsin binding and folding kinetics. Five out of the seven prosegment residues examined yielded relatively large kinetic effects and minimal ground state perturbations upon mutation, findings which indicate that these residues form strengthened and/or non-native contacts in the transition state. These five residues are semi- to strictly conserved, while only a non-conserved residue had no kinetic effect. One conserved residue was shown to form native structure in the transition state. These results indicated that the prosegment, which is only 44 residues long, has evolved a high density of contacts that preferentially stabilize the folding transition state over the ground states. It is postulated that the prosegment forms extensive non-native contacts during the process of catalyzing correct inter- and intra-domain contacts during the final stages of folding. These results have implications for understanding the folding of multi-domain proteins and for the evolution of prosegment-catalyzed folding.
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Affiliation(s)
- Derek R. Dee
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Yasumi Horimoto
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Rickey Y. Yada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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13
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Debès C, Wang M, Caetano-Anollés G, Gräter F. Evolutionary optimization of protein folding. PLoS Comput Biol 2013; 9:e1002861. [PMID: 23341762 PMCID: PMC3547816 DOI: 10.1371/journal.pcbi.1002861] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 11/09/2012] [Indexed: 01/07/2023] Open
Abstract
Nature has shaped the make up of proteins since their appearance, 3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last 1.5 billion years that began during the “big bang” of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. Nature has come up with an enormous variety of protein three-dimensional structures, each of which is thought to be optimized for its specific function. A fundamental biological endeavor is to uncover the driving evolutionary forces for discovering and optimizing new folds. A long-standing hypothesis is that fold evolution obeys constraints to properly fold into native structure. We here test this hypothesis by analyzing trends of proteins to fold fast during evolution. Using phylogenomic and structural analyses, we observe an overall decrease in folding times between 3.8 and 1.5 billion years ago, which can be interpreted as an evolutionary optimization for rapid folding. This trend towards fast folding probably resulted in manifold advantages, including high protein accessibility for the cell and a reduction of protein aggregation during misfolding.
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Affiliation(s)
- Cédric Debès
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Minglei Wang
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail: (GCA); (FG)
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
- * E-mail: (GCA); (FG)
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14
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Pauwels K, Sanchez del Pino MM, Feller G, Van Gelder P. Decoding the folding of Burkholderia glumae lipase: folding intermediates en route to kinetic stability. PLoS One 2012; 7:e36999. [PMID: 22615867 PMCID: PMC3352829 DOI: 10.1371/journal.pone.0036999] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/11/2012] [Indexed: 12/20/2022] Open
Abstract
The lipase produced by Burkholderia glumae folds spontaneously into an inactive near-native state and requires a periplasmic chaperone to reach its final active and secretion-competent fold. The B. glumae lipase-specific foldase (Lif) is classified as a member of the steric-chaperone family of which the propeptides of α-lytic protease and subtilisin are the best known representatives. Steric chaperones play a key role in conferring kinetic stability to proteins. However, until present there was no solid experimental evidence that Lif-dependent lipases are kinetically trapped enzymes. By combining thermal denaturation studies with proteolytic resistance experiments and the description of distinct folding intermediates, we demonstrate that the native lipase has a kinetically stable conformation. We show that a newly discovered molten globule-like conformation has distinct properties that clearly differ from those of the near-native intermediate state. The folding fingerprint of Lif-dependent lipases is put in the context of the protease-prodomain system and the comparison reveals clear differences that render the lipase-Lif systems unique. Limited proteolysis unveils structural differences between the near-native intermediate and the native conformation and sets the stage to shed light onto the nature of the kinetic barrier.
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Affiliation(s)
- Kris Pauwels
- Department of Structural Biology, VIB and Vrije Universiteit Brussel, Brussels, Belgium.
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Dunn IS. RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems. J Theor Biol 2011; 284:32-41. [PMID: 21703277 DOI: 10.1016/j.jtbi.2011.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 05/23/2011] [Accepted: 06/08/2011] [Indexed: 10/18/2022]
Abstract
The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical DRT systems. Beyond covalent molecular assembly, an extension of the DRT concept can include RNA molecules acting as dynamic structural template guides for the specific non-covalent assembly of multi-subunit complexes, equivalent to structural assembly chaperones. However, despite numerous precedents for RNA molecules acting as scaffolds for protein complexes, true RNA-mediated assembly chaperoning appears to be absent in modern biosystems. Another level of function with parallels to a DRT system is possible if RNA structural motifs dynamically guided specific patterns of catalytic modifications within multiple target sites in a pre-formed polymer or macromolecular complex. It is suggested that this type of structural RNA templating could logically play a functional role in certain areas of biology, one of which is the glycome of complex organisms. If any such RNA templating processes are shown to exist, they would share no necessary evolutionary relationships with events during early molecular evolution, but may promote understanding of the practical limits of biological RNA functions now and in the ancient RNA World. Awareness of these formal possibilities may also assist in the current search for functions of extensive non-coding RNAs in complex organisms, or for efforts towards artificial rendering of DRT systems.
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Affiliation(s)
- Ian S Dunn
- CytoCure LLC, 100 Cummings Center, Beverly, MA 01915, USA.
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Allen WJ, Phan G, Waksman G. Structural biology of periplasmic chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 78:51-97. [PMID: 20663484 DOI: 10.1016/s1876-1623(08)78003-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proteins often require specific helper proteins, chaperones, to assist with their correct folding and to protect them from denaturation and aggregation. The cell envelope of Gram-negative bacteria provides a particularly challenging environment for chaperones to function in as it lacks readily available energy sources such as adenosine 5' triphosphate (ATP) to power reaction cycles. Periplasmic chaperones have therefore evolved specialized mechanisms to carry out their functions without the input of external energy and in many cases to transduce energy provided by protein folding or ATP hydrolysis at the inner membrane. Structural and biochemical studies have in recent years begun to elucidate the specific functions of many important periplasmic chaperones and how these functions are carried out. This includes not only specific carrier chaperones, such as those involved in the biosynthesis of adhesive fimbriae in pathogenic bacteria, but also more general pathways including the periplasmic transport of outer membrane proteins and the extracytoplasmic stress responses. This chapter aims to provide an overview of protein chaperones so far identified in the periplasm and how structural biology has assisted with the elucidation of their functions.
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Affiliation(s)
- William J Allen
- Institute of Structural and Molecular Biology, Birkbeck and University College London, London WC1E 7HX, UK
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Sawaishi Y. Review of Alexander disease: beyond the classical concept of leukodystrophy. Brain Dev 2009; 31:493-8. [PMID: 19386454 DOI: 10.1016/j.braindev.2009.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 03/18/2009] [Accepted: 03/22/2009] [Indexed: 11/28/2022]
Abstract
Alexander disease is classified as one of the leukodystrophies, which are degenerative diseases primarily affecting the cerebral white matter. Formal diagnosis is achieved by showing diffuse accumulation of Rosenthal fibers in the brain by biopsy or autopsy. Showing a heterozygous mutation in the glial fibrillary acidic protein (GFAP) gene is currently sufficient for diagnosis. The mechanisms of Rosenthal fiber formation remain unclear. However, both the quality and quantity of GFAP are important. GFAP-epsilon (rodent homologous GFAP-delta), one of the alternatively spliced GFAP isoforms, may also play a modulating role in aggregate formation. The current ease of diagnosis has accelerated the accumulation of a wide variety of patients with Alexander disease along with the widespread use of MRI. In contrast to the classical infantile type, patients with juvenile and adult types mainly complain of bulbar symptoms and usually show progressive atrophy of the lower brainstem and cervical spinal cord with mild or minimal leukodystrophic changes. Among the many MRI findings of Alexander disease, periventricular linear lesions with various names depending on the thickness and shape seem to represent the unique pathophysiology, because the subventricular zone of the adult human brain includes special astrocytes that behave as multipotent progenitor cells and specifically produce GFAP-epsilon. Except for a few mutations, no clear phenotype-genotype correlation has been established for Alexander disease, although male preponderance in the infantile type suggests that phenotypes may be partly affected by gender.
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Affiliation(s)
- Yukio Sawaishi
- Department of Pediatrics, Akita University School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan.
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Brotherhood P, Luck I, Blake I, Jensen P, Turner P, Crossley M. Regioselective Reactivity of an Asymmetric Tetravalent Di[dihydroxotin(IV)] Bis-Porphyrin Host Driven by Hydrogen-Bond Templation. Chemistry 2008; 14:10967-77. [DOI: 10.1002/chem.200801775] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Pauwels K, Van Gelder P. Affinity-based isolation of a bacterial lipase through steric chaperone interactions. Protein Expr Purif 2008; 59:342-8. [DOI: 10.1016/j.pep.2008.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Accepted: 03/02/2008] [Indexed: 10/22/2022]
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Self-replicating protein conformations and information transfer: The adaptive β-sheet model. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.bihy.2008.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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