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A proteome-wide map of chaperone-assisted protein refolding in a cytosol-like milieu. Proc Natl Acad Sci U S A 2022; 119:e2210536119. [PMID: 36417429 PMCID: PMC9860312 DOI: 10.1073/pnas.2210536119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain's intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting many proteins safe passage to their native states; however, it is challenging to interrogate the folding process for large numbers of proteins in a complex background with most biophysical techniques. Hence, most chaperone-assisted protein refolding studies are conducted in defined buffers on single purified clients. Here, we develop a limited proteolysis-mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding Escherichia coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. We suggest that these proteins may fold most efficiently cotranslationally, and then remain kinetically trapped in their native conformations.
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2
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Shinde S, Patwardhan A, Watve M. The ratio versus difference optimization and its implications for optimality theory. Evolution 2022; 76:2272-2280. [PMID: 36029469 DOI: 10.1111/evo.14605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/29/2022] [Accepted: 08/12/2022] [Indexed: 01/22/2023]
Abstract
Among the classical models of optimization, some models maximize the ratio of returns to investment and others maximize the difference between returns and investment. However, an understanding of under what conditions the ratio or the difference approaches are appropriate is still fragmentary. Under specific contexts, it has been stated that when the investable amount, but not the opportunity for investment, is perceived to be limiting, a ratio optimum is appropriate, whereas a difference optimum is appropriate when the opportunity for investment, but not the investable amount, is perceived to be limiting. The question is important because the strategies indicated by ratio optimum can be substantially different than the ones suggested by difference optimum. We make a general case here to examine and expand this principle and apply it to many evolutionary ecological problems including parental investment, offspring quality-quantity trade-off, nectar production, pollinator behavior viral burst size, and intracellular protein handling. We show that the ratio-difference distinction in optimization models resolves many long-standing debates and conundrums in evolution and behavior.
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Affiliation(s)
- Sonali Shinde
- Annasaheb Kulkarni Department of Biodiversity, Abasaheb Garware College, Pune, 411004, India
| | - Ankur Patwardhan
- Annasaheb Kulkarni Department of Biodiversity, Abasaheb Garware College, Pune, 411004, India
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3
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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Balchin D, Hayer-Hartl M, Hartl FU. Recent advances in understanding catalysis of protein folding by molecular chaperones. FEBS Lett 2020; 594:2770-2781. [PMID: 32446288 DOI: 10.1002/1873-3468.13844] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022]
Abstract
Molecular chaperones are highly conserved proteins that promote proper folding of other proteins in vivo. Diverse chaperone systems assist de novo protein folding and trafficking, the assembly of oligomeric complexes, and recovery from stress-induced unfolding. A fundamental function of molecular chaperones is to inhibit unproductive protein interactions by recognizing and protecting hydrophobic surfaces that are exposed during folding or following proteotoxic stress. Beyond this basic principle, it is now clear that chaperones can also actively and specifically accelerate folding reactions in an ATP-dependent manner. We focus on the bacterial Hsp70 and chaperonin systems as paradigms, and review recent work that has advanced our understanding of how these chaperones act as catalysts of protein folding.
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Affiliation(s)
- David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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5
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Motojima F, Fujii K, Yoshida M. Chaperonin facilitates protein folding by avoiding initial polypeptide collapse. J Biochem 2018; 164:369-379. [PMID: 30053017 PMCID: PMC6190516 DOI: 10.1093/jb/mvy061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 07/12/2018] [Indexed: 11/14/2022] Open
Abstract
Chaperonins assist folding of many cellular proteins, including essential proteins for cell viability. However, it remains unclear how chaperonin-assisted folding is different from spontaneous folding. Chaperonin GroEL/GroES facilitates folding of denatured protein encapsulated in its central cage but the denatured protein often escapes from the cage to the outside during reaction. Here, we show evidence that the in-cage-folding and the escape occur diverging from the same intermediate complex in which polypeptide is tethered loosely to the cage and partly protrudes out of the cage. Furthermore, denatured proteins in the chaperonin cage are kept in more extended conformation than those initially formed in spontaneous folding. We propose that the formation of tethered intermediate of polypeptide is necessary to prevent polypeptide collapse at the expense of polypeptide escape. The tethering of polypeptide would allow freely mobile portions of tethered polypeptide to fold segmentally.
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Affiliation(s)
- Fumihiro Motojima
- Department of Molecular Biosciences, Kyoto Sangyo University Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Katsuya Fujii
- Department of Molecular Biosciences, Kyoto Sangyo University Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Masasuke Yoshida
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
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6
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Hayer-Hartl M. From chaperonins to Rubisco assembly and metabolic repair. Protein Sci 2017; 26:2324-2333. [PMID: 28960553 DOI: 10.1002/pro.3309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 01/13/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Despite its pivotal role, Rubisco is an inefficient enzyme and thus has been a key target for bioengineering. However, efforts to increase crop yields by Rubisco engineering remain unsuccessful, due in part to the complex machinery of molecular chaperones required for Rubisco biogenesis and metabolic repair. While the large subunit of Rubisco generally requires the chaperonin system for folding, the evolution of the hexadecameric Rubisco from its dimeric precursor resulted in the dependence on an array of additional factors required for assembly. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands. Metabolic repair of Rubisco depends on remodeling by the ATP-dependent Rubisco activase and hydrolysis of inhibitors by specific phosphatases. This review highlights our work toward understanding the structure and mechanism of these auxiliary machineries.
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Affiliation(s)
- Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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Weaver J, Jiang M, Roth A, Puchalla J, Zhang J, Rye HS. GroEL actively stimulates folding of the endogenous substrate protein PepQ. Nat Commun 2017; 8:15934. [PMID: 28665408 PMCID: PMC5497066 DOI: 10.1038/ncomms15934] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 05/13/2017] [Indexed: 12/29/2022] Open
Abstract
Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role. In the prevailing model for assisted protein folding, chaperonins act passively by preventing protein aggregation. Here, the authors use single-molecule fluorescence measurements and cryo-electron microscopy and show that the E. coli GroELS chaperonin system also has an active role in folding the endogenous bacterial protein PepQ.
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Affiliation(s)
- Jeremy Weaver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845, USA
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845, USA.,State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845, USA
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845, USA
| | - Hays S Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845, USA
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Senavirathne G, Mahto SK, Hanne J, O'Brian D, Fishel R. Dynamic unwrapping of nucleosomes by HsRAD51 that includes sliding and rotational motion of histone octamers. Nucleic Acids Res 2016; 45:685-698. [PMID: 27738136 PMCID: PMC5314800 DOI: 10.1093/nar/gkw920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/01/2016] [Accepted: 10/10/2016] [Indexed: 01/24/2023] Open
Abstract
Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine triphosphate (ATP) the human RAD51 (HsRAD51) recombinase can form a nucleoprotein filament (NPF) on double-stranded DNA (dsDNA) that is capable of unwrapping the nucleosomal DNA from the histone octamer (HO). Here, we have used single molecule Förster Resonance Energy Transfer (smFRET) to examine the real time nucleosome dynamics in the presence of the HsRAD51 NPF. We show that oligomerization of HsRAD51 leads to stepwise, but stochastic unwrapping of the DNA from the HO in the presence of ATP. The highly reversible dynamics observed in single-molecule trajectories suggests an antagonistic mechanism between HsRAD51 binding and rewrapping of the DNA around the HO. These stochastic dynamics were independent of the nucleosomal DNA sequence or the asymmetry created by the presence of a linker DNA. We also observed sliding and rotational oscillations of the HO with respect to the nucleosomal DNA. These studies underline the dynamic nature of even tightly associated protein-DNA complexes such as nucleosomes.
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Affiliation(s)
- Gayan Senavirathne
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Santosh K Mahto
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Jeungphill Hanne
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Daniel O'Brian
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA .,Physics Department, The Ohio State University, Columbus, OH 43210, USA
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9
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Replacement of GroEL in Escherichia coli by the Group II Chaperonin from the Archaeon Methanococcus maripaludis. J Bacteriol 2016; 198:2692-700. [PMID: 27432832 PMCID: PMC5019054 DOI: 10.1128/jb.00317-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/23/2016] [Indexed: 12/21/2022] Open
Abstract
Chaperonins are required for correct folding of many proteins. They exist in two phylogenetic groups: group I, found in bacteria and eukaryotic organelles, and group II, found in archaea and eukaryotic cytoplasm. The two groups, while homologous, differ significantly in structure and mechanism. The evolution of group II chaperonins has been proposed to have been crucial in enabling the expansion of the proteome required for eukaryotic evolution. In an archaeal species that expresses both groups of chaperonins, client selection is determined by structural and biochemical properties rather than phylogenetic origin. It is thus predicted that group II chaperonins will be poor at replacing group I chaperonins. We have tested this hypothesis and report here that the group II chaperonin from Methanococcus maripaludis (Mm-cpn) can partially functionally replace GroEL, the group I chaperonin of Escherichia coli. Furthermore, we identify and characterize two single point mutations in Mm-cpn that have an enhanced ability to replace GroEL function, including one that allows E. coli growth after deletion of the groEL gene. The biochemical properties of the wild-type and mutant Mm-cpn proteins are reported. These data show that the two groups are not as functionally diverse as has been thought and provide a novel platform for genetic dissection of group II chaperonins. IMPORTANCE The two phylogenetic groups of the essential and ubiquitous chaperonins diverged approximately 3.7 billion years ago. They have similar structures, with two rings of multiple subunits, and their major role is to assist protein folding. However, they differ with regard to the details of their structure, their cofactor requirements, and their reaction cycles. Despite this, we show here that a group II chaperonin from a methanogenic archaeon can partially substitute for the essential group I chaperonin GroEL in E. coli and that we can easily isolate mutant forms of this chaperonin with further improved functionality. This is the first demonstration that these two groups, despite the long time since they diverged, still overlap significantly in their functional properties.
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10
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Potnis AA, Rajaram H, Apte SK. GroEL of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31 exhibits GroES and ATP-independent refolding activity. J Biochem 2015; 159:295-304. [PMID: 26449235 DOI: 10.1093/jb/mvv100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
The nitrogen-fixing cyanobacterium, Anabaena L-31 has two Hsp60 proteins, 59 kDa GroEL coded by the second gene of groESL operon and 61 kDa Cpn60 coded by cpn60 gene. Anabaena GroEL formed stable higher oligomer (>12-mer) in the presence of K(+) and prevented thermal aggregation of malate dehydrogenase (MDH). Using three protein substrates (MDH, All1541 and green fluorescent protein), it was found that the refolding activity of Anabaena GroEL was lower than that of Escherichia coli GroEL, but independent of both GroES and ATP. This correlated with in vivo data. GroEL exhibited ATPase activity which was enhanced in the presence of GroES and absence of a denatured protein, contrary to that observed for bacterial GroEL. However, a significant role for ATP could not be ascertained during in vitro folding assays. The monomeric Cpn60 exhibited much lower refolding activity than GroEL, unaffected by GroES and ATP. In vitro studies revealed inhibition of the refolding activity of Anabaena GroEL by Cpn60, which could be due to their different oligomeric status. The role of GroES and ATP may have been added during the course of evolution from the ancient cyanobacteria to modern day bacteria enhancing the refolding ability and ensuring wider scope of substrates for GroEL.
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Affiliation(s)
- Akhilesh A Potnis
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Shree K Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
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11
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Gao L, Imanaka T, Fujiwara S. A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions. J Bacteriol 2015; 197:2642-52. [PMID: 26013483 PMCID: PMC4507335 DOI: 10.1128/jb.00279-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Thermococcus kodakarensis grows optimally at 85°C and possesses two chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. The two chaperonins share a high sequence identity (77%), except in their C-terminal regions. CpkA, which contains tandem repeats of a GGM motif, shows its highest ATPase activity at 60°C to 70°C, whereas CpkB shows its highest activity at temperatures higher than 90°C. To clarify the effects of changes in ATPase activity on chaperonin function at lower temperatures, various CpkA variants were constructed by introducing single point mutations into the C-terminal region. A CpkA variant in which Glu530 was replaced with Gly (CpkA-E530G) showed increased ATPase activity, with its highest activity at 50°C. The efficacy of the CpkA variants against denatured indole-3-glycerol-phosphate synthase of T. kodakarensis (TrpCTk), which is a CpkA target, was then examined in vitro. CpkA-E530G was more effective than wild-type CpkA at facilitating the refolding of chemically unfolded TrpCTk at 50°C. The effect of cpkA-E530G on cell growth was then examined by introducing cpkA-E530G into the genome of T. kodakarensis KU216 (pyrF). The mutant strain, DA4 (pyrF cpkA-E530G), grew as well as the parental KU216 strain at 60°C. In contrast, DA4 grew more vigorously than KU216 at 50°C. These results suggested that the CpkA-E530G mutation prevented cold denaturation of proteins under cold-stress conditions, thereby enabling cells to grow in cooler environments. Thus, a single base pair substitution in a chaperonin gene allows cells to grow vigorously in a new environment. IMPORTANCE Thermococcus kodakarensis possesses two group II chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. CpkA might act as an "adaptive allele" to adapt to cooler environments. In this study, we compared the last 20 amino acids within the C termini of the chaperonins and found a clear correlation between the CpkA-type chaperonin gene copy number and growth temperature. Furthermore, we introduced single mutations into the CpkA C-terminal region to clarify its role in cold adaptation, and we showed that a single base substitution allowed the organism to adapt to a lower temperature. The present data suggest that hyperthermophiles have evolved by obtaining mutations in chaperonins that allow them to adapt to a colder environment.
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Affiliation(s)
- Le Gao
- Research Center for Intelligent Bio-Materials, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Kasatsu, Shiga, Japan
| | - Shinsuke Fujiwara
- Research Center for Intelligent Bio-Materials, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, Japan
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Kumar CMS, Mande SC, Mahajan G. Multiple chaperonins in bacteria--novel functions and non-canonical behaviors. Cell Stress Chaperones 2015; 20:555-74. [PMID: 25986150 PMCID: PMC4463927 DOI: 10.1007/s12192-015-0598-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/05/2023] Open
Abstract
Chaperonins are a class of molecular chaperones that assemble into a large double ring architecture with each ring constituting seven to nine subunits and enclosing a cavity for substrate encapsulation. The well-studied Escherichia coli chaperonin GroEL binds non-native substrates and encapsulates them in the cavity thereby sequestering the substrates from unfavorable conditions and allowing the substrates to fold. Using this mechanism, GroEL assists folding of about 10-15 % of cellular proteins. Surprisingly, about 30 % of the bacteria express multiple chaperonin genes. The presence of multiple chaperonins raises questions on whether they increase general chaperoning ability in the cell or have developed specific novel cellular roles. Although the latter view is widely supported, evidence for the former is beginning to appear. Some of these chaperonins can functionally replace GroEL in E. coli and are generally indispensable, while others are ineffective and likewise are dispensable. Additionally, moonlighting functions for several chaperonins have been demonstrated, indicating a functional diversity among the chaperonins. Furthermore, proteomic studies have identified diverse substrate pools for multiple chaperonins. We review the current perception on multiple chaperonins and their physiological and functional specificities.
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Affiliation(s)
- C M Santosh Kumar
- Laboratory of Structural Biology, National Centre for Cell Science, Pune, 411007, India,
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13
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Abstract
Protein folding is a biological process that is essential for the proper functioning of proteins in all living organisms. In cells, many proteins require the assistance of molecular chaperones for their folding. Chaperonins belong to a class of molecular chaperones that have been extensively studied. However, the mechanism by which a chaperonin mediates the folding of proteins is still controversial. Denatured proteins are folded in the closed chaperonin cage, leading to the assumption that denatured proteins are completely encapsulated inside the chaperonin cage. In contrast to the assumption, we recently found that denatured protein interacts with hydrophobic residues at the subunit interfaces of the chaperonin, and partially protrude out of the cage. In this review, we will explain our recent results and introduce our model for the mechanism by which chaperonins accelerate protein folding, in view of recent findings.
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Affiliation(s)
- Fumihiro Motojima
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
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14
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GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding. Cell 2014; 157:922-934. [PMID: 24813614 DOI: 10.1016/j.cell.2014.03.038] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/04/2014] [Accepted: 03/14/2014] [Indexed: 11/23/2022]
Abstract
The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (βα)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. Here, we analyzed the folding of DapA at peptide resolution using hydrogen/deuterium exchange and mass spectrometry. During spontaneous folding, all elements of the DapA TIM barrel acquire structure simultaneously in a process associated with a long search time. In contrast, GroEL/ES accelerates folding more than 30-fold by catalyzing segmental structure formation in the TIM barrel. Segmental structure formation is also observed during the fast spontaneous folding of a structural homolog of DapA from a bacterium that lacks GroEL/ES. Thus, chaperonin independence correlates with folding properties otherwise enforced by protein confinement in the GroEL/ES cage. We suggest that folding catalysis by GroEL/ES is required by a set of proteins to reach native state at a biologically relevant timescale, avoiding aggregation or degradation.
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15
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Weaver J, Rye HS. The C-terminal tails of the bacterial chaperonin GroEL stimulate protein folding by directly altering the conformation of a substrate protein. J Biol Chem 2014; 289:23219-23232. [PMID: 24970895 DOI: 10.1074/jbc.m114.577205] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many essential cellular proteins fold only with the assistance of chaperonin machines like the GroEL-GroES system of Escherichia coli. However, the mechanistic details of assisted protein folding by GroEL-GroES remain the subject of ongoing debate. We previously demonstrated that GroEL-GroES enhances the productive folding of a kinetically trapped substrate protein through unfolding, where both binding energy and the energy of ATP hydrolysis are used to disrupt the inhibitory misfolded states. Here, we show that the intrinsically disordered yet highly conserved C-terminal sequence of the GroEL subunits directly contributes to substrate protein unfolding. Interactions between the C terminus and the non-native substrate protein alter the binding position of the substrate protein on the GroEL apical surface. The C-terminal tails also impact the conformational state of the substrate protein during capture and encapsulation on the GroEL ring. Importantly, removal of the C termini results in slower overall folding, reducing the fraction of the substrate protein that commits quickly to a productive folding pathway and slowing several kinetically distinct folding transitions that occur inside the GroEL-GroES cavity. The conserved C-terminal tails of GroEL are thus important for protein folding from the beginning to the end of the chaperonin reaction cycle.
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Affiliation(s)
- Jeremy Weaver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Hays S Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843.
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16
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Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem 2013; 82:323-55. [PMID: 23746257 DOI: 10.1146/annurev-biochem-060208-092442] [Citation(s) in RCA: 997] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The biological functions of proteins are governed by their three-dimensional fold. Protein folding, maintenance of proteome integrity, and protein homeostasis (proteostasis) critically depend on a complex network of molecular chaperones. Disruption of proteostasis is implicated in aging and the pathogenesis of numerous degenerative diseases. In the cytosol, different classes of molecular chaperones cooperate in evolutionarily conserved folding pathways. Nascent polypeptides interact cotranslationally with a first set of chaperones, including trigger factor and the Hsp70 system, which prevent premature (mis)folding. Folding occurs upon controlled release of newly synthesized proteins from these factors or after transfer to downstream chaperones such as the chaperonins. Chaperonins are large, cylindrical complexes that provide a central compartment for a single protein chain to fold unimpaired by aggregation. This review focuses on recent advances in understanding the mechanisms of chaperone action in promoting and regulating protein folding and on the pathological consequences of protein misfolding and aggregation.
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Affiliation(s)
- Yujin E Kim
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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Ong DST, Wang YJ, Tan YL, Yates JR, Mu TW, Kelly JW. FKBP10 depletion enhances glucocerebrosidase proteostasis in Gaucher disease fibroblasts. ACTA ACUST UNITED AC 2013; 20:403-15. [PMID: 23434032 DOI: 10.1016/j.chembiol.2012.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 12/20/2022]
Abstract
Lysosomal storage diseases (LSDs) are often caused by mutations compromising lysosomal enzyme folding in the endoplasmic reticulum (ER), leading to degradation and loss of function. Mass spectrometry analysis of Gaucher fibroblasts treated with mechanistically distinct molecules that increase LSD enzyme folding, trafficking, and function resulted in the identification of nine commonly downregulated and two jointly upregulated proteins, which we hypothesized would be critical proteostasis network components for ameliorating loss-of-function diseases. LIMP-2 and FK506 binding protein 10 (FKBP10) were validated as such herein. Increased FKBP10 levels accelerated mutant glucocerebrosidase degradation over folding and trafficking, whereas decreased ER FKBP10 concentration led to more LSD enzyme partitioning into the calnexin profolding pathway, enhancing folding and activity to levels thought to ameliorate LSDs. Thus, targeting FKBP10 appears to be a heretofore unrecognized therapeutic strategy to ameliorate LSDs.
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Affiliation(s)
- Derrick Sek Tong Ong
- Departments of Chemistry and Molecular and Experimental Medicine and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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18
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White AD, Huang W, Jiang S. Role of nonspecific interactions in molecular chaperones through model-based bioinformatics. Biophys J 2012; 103:2484-91. [PMID: 23260050 DOI: 10.1016/j.bpj.2012.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/22/2012] [Accepted: 10/31/2012] [Indexed: 01/16/2023] Open
Abstract
Molecular chaperones are large proteins or protein complexes from which many proteins require assistance in order to fold. One unique property of molecular chaperones is the cavity they provide in which proteins fold. The interior surface residues which make up the cavities of molecular chaperone complexes from different organisms has recently been identified, including the well-studied GroEL-GroES chaperonin complex found in Escherichia coli. It was found that the interior of these protein complexes is significantly different than other protein surfaces and that the residues found on the protein surface are able to resist protein adsorption when immobilized on a surface. Yet it remains unknown if these residues passively resist protein binding inside GroEL-GroEs (as demonstrated by experiments that created synthetic mimics of the interior cavity) or if the interior also actively stabilizes protein folding. To answer this question, we have extended entropic models of substrate protein folding inside GroEL-GroES to include interaction energies between substrate proteins and the GroEL-GroES chaperone complex. This model was tested on a set of 528 proteins and the results qualitatively match experimental observations. The interior residues were found to strongly discourage the exposure of any hydrophobic residues, providing an enhanced hydrophobic effect inside the cavity that actively influences protein folding. This work provides both a mechanism for active protein stabilization in GroEL-GroES and a model that matches contemporary understanding of the chaperone protein.
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Affiliation(s)
- Andrew D White
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
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19
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Yamauchi S, Ueda Y, Matsumoto M, Inoue U, Hayashi H. Distinct features of protein folding by the GroEL system from a psychrophilic bacterium, Colwellia psychrerythraea 34H. Extremophiles 2012; 16:871-82. [PMID: 22996829 DOI: 10.1007/s00792-012-0483-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/09/2012] [Indexed: 01/28/2023]
Abstract
We investigated the protein folding mechanism of the GroEL system of a psychrophilic bacterium, Colwellia psychrerythraea 34H. The amount of mRNA of the groESL operon of C. psychrerythraea was increased about 6-fold after a temperature upshift from 8 to 18 °C for 30 min, suggesting that this temperature causes heat stress in this bacterium. A σ(32)-type promoter was found upstream of the groESL, suggesting that the C. psychrerythraea groESL is regulated by the σ(32) system, like the groESL in E. coli. The maximum ATPase and CTPase activities of CpGroEL were observed at 45 and 35 °C, respectively, which are much higher than the growth temperatures of C. psychrerythraea. We found that the refolding activity of the CpGroEL system in the presence of ATP is lower than that in the presence of CTP. This suggests that ATP is not the optimum energy source of the CpGroEL system. Analyses for the interaction of CpGroEL-CpGroES revealed that CTP could weaken this interaction, resulting in effective refolding function of the CpGroEL system. From these findings, we consider that the CpGroEL system possesses an energy-saving mechanism for avoiding excess consumption of ATP to ensure growth in a low-temperature environment.
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Affiliation(s)
- Seiji Yamauchi
- Cell-Free Science and Technology Research Center, Ehime University, 3 Bunkyo-cho, Matsuyama, 790-8577, Japan.
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20
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Revisiting the contribution of negative charges on the chaperonin cage wall to the acceleration of protein folding. Proc Natl Acad Sci U S A 2012; 109:15740-5. [PMID: 22961256 DOI: 10.1073/pnas.1204547109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chaperonin GroEL mediates the folding of protein encapsulated in a GroES-sealed cavity (cage). Recently, a critical role of negative charge clusters on the cage wall in folding acceleration was proposed based on experiments using GroEL single-ring (SR) mutants SR1 and SRKKK2 [Tang YC, et al. (2006) Cell 125:903-914; Chakraborty K, et al. (2010) Cell 142:112-122]. Here, we revisited these experiments and discovered several inconsistencies. (i) SR1 was assumed to bind to GroES stably and to mediate single-round folding in the cage. However, we show that SR1 repeats multiple turnovers of GroES release/binding coupled with ATP hydrolysis. (ii) Although the slow folding observed for a double-mutant of maltose binding protein (DMMBP) by SRKKK2 was attributed to mutations that neutralize negative charges on the cage wall, we found that the majority of DMMBP escape from SRKKK2 and undergo spontaneous folding in the bulk medium. (iii) An osmolyte, trimethylamine N-oxide, was reported to accelerate SRKKK2-mediated folding of DMMBP by mimicking the effect of cage-wall negative charges of WT GroEL and ordering the water structure to promote protein compaction. However, we demonstrate that in-cage folding by SRKKK2 is unaffected by trimethylamine N-oxide. (iv) Although it was reported that SRKKK2 lost the ability to assist the folding of ribulose-1,5-bisphosphate carboxylase/oxygenase, we found that SRKKK2 retains this ability. Our results argue against the role of the negative charges on the cage wall of GroEL in protein folding. Thus, in chaperonin studies, folding kinetics need to be determined from the fraction of the real in-cage folding.
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21
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Billerbeck S, Panke S. A genetic replacement system for selection-based engineering of essential proteins. Microb Cell Fact 2012; 11:110. [PMID: 22898007 PMCID: PMC3503863 DOI: 10.1186/1475-2859-11-110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/08/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Essential genes represent the core of biological functions required for viability. Molecular understanding of essentiality as well as design of synthetic cellular systems includes the engineering of essential proteins. An impediment to this effort is the lack of growth-based selection systems suitable for directed evolution approaches. RESULTS We established a simple strategy for genetic replacement of an essential gene by a (library of) variant(s) during a transformation.The system was validated using three different essential genes and plasmid combinations and it reproducibly shows transformation efficiencies on the order of 107 transformants per microgram of DNA without any identifiable false positives. This allowed for reliable recovery of functional variants out of at least a 105-fold excess of non-functional variants. This outperformed selection in conventional bleach-out strains by at least two orders of magnitude, where recombination between functional and non-functional variants interfered with reliable recovery even in recA negative strains. CONCLUSIONS We propose that this selection system is extremely suitable for evaluating large libraries of engineered essential proteins resulting in the reliable isolation of functional variants in a clean strain background which can readily be used for in vivo applications as well as expression and purification for use in in vitro studies.
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Affiliation(s)
- Sonja Billerbeck
- ETH Zürich, Department for Biosystems Science and Engineering (D-BSSE), Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- ETH Zürich, Department for Biosystems Science and Engineering (D-BSSE), Mattenstrasse 26, 4058, Basel, Switzerland
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22
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Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure 2012; 20:814-25. [PMID: 22503819 PMCID: PMC3350567 DOI: 10.1016/j.str.2012.03.007] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 01/27/2023]
Abstract
TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. Previously proposed TRiC models differ substantially in their subunit arrangements and ring register. Here, we integrate chemical crosslinking, mass spectrometry, and combinatorial modeling to reveal the definitive subunit arrangement of TRiC. In vivo disulfide mapping provided additional validation for the crosslinking-derived arrangement as the definitive TRiC topology. This subunit arrangement allowed the refinement of a structural model using existing X-ray diffraction data. The structure described here explains all available crosslink experiments, provides a rationale for previously unexplained structural features, and reveals a surprising asymmetry of charges within the chaperonin folding chamber.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Leonie Mönkemeyer
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Ph.D. Program in Molecular Life Sciences, University of Zurich/ETH Zurich 8057 Zurich, Switzerland
| | - Bryan Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Yao Cong
- National Center for Macromolecular Imaging; Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine, Houston, TX 77030, USA
| | - Boxue Ma
- National Center for Macromolecular Imaging; Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine, Houston, TX 77030, USA
| | - Steve Ludtke
- National Center for Macromolecular Imaging; Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging; Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine, Houston, TX 77030, USA
| | - F. Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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23
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Love AC. Hierarchy, causation and explanation: ubiquity, locality and pluralism. Interface Focus 2012; 2:115-25. [PMID: 23386966 PMCID: PMC3262310 DOI: 10.1098/rsfs.2011.0064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/24/2011] [Indexed: 11/12/2022] Open
Abstract
The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified 'levels' of organization and suggests that attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily 'local' and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended-many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry.
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Affiliation(s)
- Alan C. Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, 831 Heller Hall, 271 19th Ave. S, Minneapolis, MN 55455-0310, USA
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24
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Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach. PLoS One 2011; 6:e28329. [PMID: 22174789 PMCID: PMC3234253 DOI: 10.1371/journal.pone.0028329] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 11/05/2011] [Indexed: 01/08/2023] Open
Abstract
Background Rhodopseudomonas palustris (R. palustris) is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin–Benson–Bassham (CBB) cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. Methodology/Principal Findings By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM) but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC) strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. Conclusions/Significance Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth through both common and divergent metabolic mechanisms.
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25
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Lindquist SL, Kelly JW. Chemical and biological approaches for adapting proteostasis to ameliorate protein misfolding and aggregation diseases: progress and prognosis. Cold Spring Harb Perspect Biol 2011; 3:a004507. [PMID: 21900404 PMCID: PMC3225948 DOI: 10.1101/cshperspect.a004507] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Maintaining the proteome to preserve the health of an organism in the face of developmental changes, environmental insults, infectious diseases, and rigors of aging is a formidable task. The challenge is magnified by the inheritance of mutations that render individual proteins subject to misfolding and/or aggregation. Maintenance of the proteome requires the orchestration of protein synthesis, folding, degradation, and trafficking by highly conserved/deeply integrated cellular networks. In humans, no less than 2000 genes are involved. Stress sensors detect the misfolding and aggregation of proteins in specific organelles and respond by activating stress-responsive signaling pathways. These culminate in transcriptional and posttranscriptional programs that up-regulate the homeostatic mechanisms unique to that organelle. Proteostasis is also strongly influenced by the general properties of protein folding that are intrinsic to every proteome. These include the kinetics and thermodynamics of the folding, misfolding, and aggregation of individual proteins. We examine a growing body of evidence establishing that when cellular proteostasis goes awry, it can be reestablished by deliberate chemical and biological interventions. We start with approaches that employ chemicals or biological agents to enhance the general capacity of the proteostasis network. We then introduce chemical approaches to prevent the misfolding or aggregation of specific proteins through direct binding interactions. We finish with evidence that synergy is achieved with the combination of mechanistically distinct approaches to reestablish organismal proteostasis.
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Affiliation(s)
- Susan L Lindquist
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA.
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26
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A chaperonin subunit with unique structures is essential for folding of a specific substrate. PLoS Biol 2011; 9:e1001040. [PMID: 21483722 PMCID: PMC3071376 DOI: 10.1371/journal.pbio.1001040] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 02/23/2011] [Indexed: 01/01/2023] Open
Abstract
Type I chaperonins are large, double-ring complexes present in bacteria (GroEL),
mitochondria (Hsp60), and chloroplasts (Cpn60), which are involved in mediating
the folding of newly synthesized, translocated, or stress-denatured proteins. In
Escherichia coli, GroEL comprises 14 identical subunits and
has been exquisitely optimized to fold its broad range of substrates. However,
multiple Cpn60 subunits with different expression profiles have evolved in
chloroplasts. Here, we show that, in Arabidopsis thaliana, the
minor subunit Cpn60β4 forms a heterooligomeric Cpn60 complex with
Cpn60α1 and Cpn60β1–β3 and is specifically required for the
folding of NdhH, a subunit of the chloroplast NADH dehydrogenase-like complex
(NDH). Other Cpn60β subunits cannot complement the function of Cpn60β4.
Furthermore, the unique C-terminus of Cpn60β4 is required for the full
activity of the unique Cpn60 complex containing Cpn60β4 for folding of NdhH.
Our findings suggest that this unusual kind of subunit enables the Cpn60 complex
to assist the folding of some particular substrates, whereas other dominant
Cpn60 subunits maintain a housekeeping chaperonin function by facilitating the
folding of other obligate substrates. Chaperonins assist the folding of some nascent and denatured proteins to their
native, functional forms. Each chaperonin consists of a pair of protein
complexes resembling two stacked toroids; folding occurs inside the toroid
cavity. Chaperonins are ubiquitous in both bacteria and more complex nucleated
cells, as well as in the intracellular organelles that have evolved from
bacteria by endosymbiosis: mitochondria and, in plants, chloroplasts. They are
indispensable for cellular function. Many different chaperonin subunits have
evolved in various species of bacteria as well as in most mitochondria and
chloroplasts. The physiological and functional relevance of these multiple
chaperonin subunits is poorly understood, however. In this study, we have
characterized the minor chaperonin subunit Cpn60β4 from
Arabidopsis chloroplasts, which differs in structure from
other chloroplast chaperonins. When the Cpn60β4 gene is
defective, the plants fail to accumulate one protein complex in particular: the
chloroplast NADH dehydrogenase-like complex (NDH). We discovered that
Cpn60β4 forms a complex with other Cpn60 α and β
subunits and that this complex is essential for the folding of the NDH subunit
NdhH. Cpn60β4 has a unique protein “tail” that is required for
the efficient folding of NdhH. Our findings suggest that Cpn60β4 has evolved
with distinctive structural features that facilitate the folding of one specific
substrate and that this strategy is used by plants to satisfy their conflicting
requirements for chaperonins with both specialized and general functions.
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27
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Vabulas RM, Raychaudhuri S, Hayer-Hartl M, Hartl FU. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2011; 2:a004390. [PMID: 21123396 DOI: 10.1101/cshperspect.a004390] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins generally must fold into precise three-dimensional conformations to fulfill their biological functions. In the cell, this fundamental process is aided by molecular chaperones, which act in preventing protein misfolding and aggregation. How this machinery assists newly synthesized polypeptide chains in navigating the complex folding energy landscape is now being understood in considerable detail. The mechanisms that ensure the maintenance of a functional proteome under normal and stress conditions are also of great medical relevance, as the aggregation of proteins that escape the cellular quality control underlies a range of debilitating diseases, including many age-of-onset neurodegenerative disorders.
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Affiliation(s)
- R Martin Vabulas
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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28
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Chemical and/or biological therapeutic strategies to ameliorate protein misfolding diseases. Curr Opin Cell Biol 2010; 23:231-8. [PMID: 21146391 DOI: 10.1016/j.ceb.2010.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 11/16/2010] [Indexed: 12/22/2022]
Abstract
Inheriting a mutant misfolding-prone protein that cannot be efficiently folded in a given cell type(s) results in a spectrum of human loss-of-function misfolding diseases. The inability of the biological protein maturation pathways to adapt to a specific misfolding-prone protein also contributes to pathology. Chemical and biological therapeutic strategies are presented that restore protein homeostasis, or proteostasis, either by enhancing the biological capacity of the proteostasis network or through small molecule stabilization of a specific misfolding-prone protein. Herein, we review the recent literature on therapeutic strategies to ameliorate protein misfolding diseases that function through either of these mechanisms, or a combination thereof, and provide our perspective on the promise of alleviating protein misfolding diseases by taking advantage of proteostasis adaptation.
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29
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Ong DST, Mu TW, Palmer AE, Kelly JW. Endoplasmic reticulum Ca2+ increases enhance mutant glucocerebrosidase proteostasis. Nat Chem Biol 2010; 6:424-32. [PMID: 20453863 PMCID: PMC2873071 DOI: 10.1038/nchembio.368] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 03/04/2010] [Indexed: 12/22/2022]
Abstract
Altering intracellular calcium levels is known to partially restore mutant enzyme homeostasis in several lysosomal storage diseases, but why? We hypothesize that endoplasmic reticulum (ER) calcium level increases enhance the folding, trafficking and function of these mutant misfolding/degradation-prone lysosomal enzymes by increasing chaperone function. Herein, we report that increasing ER calcium levels by reducing ER calcium efflux through the ryanodine receptor (antagonists or RNAi) or by promoting ER calcium influx by SERCA2b overexpression enhances mutant glucocerebrosidase (GC) homeostasis in Gaucher’s disease patient-derived cells. Post-translational regulation of the calnexin folding pathway by increasing the ER calcium concentration appears to enhance the capacity of this chaperone system to fold mutant misfolding-prone enzymes, increasing the folded mutant GC population that can engage the trafficking receptor at the expense of ER-associated degradation, increasing the lysosomal GC concentration.
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Affiliation(s)
- Derrick Sek Tong Ong
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
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30
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A systematic survey of in vivo obligate chaperonin-dependent substrates. EMBO J 2010; 29:1552-64. [PMID: 20360681 DOI: 10.1038/emboj.2010.52] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 03/08/2010] [Indexed: 01/17/2023] Open
Abstract
Chaperonins are absolutely required for the folding of a subset of proteins in the cell. An earlier proteome-wide analysis of Escherichia coli chaperonin GroEL/GroES (GroE) interactors predicted obligate chaperonin substrates, which were termed Class III substrates. However, the requirement of chaperonins for in vivo folding has not been fully examined. Here, we comprehensively assessed the chaperonin requirement using a conditional GroE expression strain, and concluded that only approximately 60% of Class III substrates are bona fide obligate GroE substrates in vivo. The in vivo obligate substrates, combined with the newly identified obligate substrates, were termed Class IV substrates. Class IV substrates are restricted to proteins with molecular weights that could be encapsulated in the chaperonin cavity, are enriched in alanine/glycine residues, and have a strong structural preference for aggregation-prone folds. Notably, approximately 70% of the Class IV substrates appear to be metabolic enzymes, supporting a hypothetical role of GroE in enzyme evolution.
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31
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Elcock AH. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 2010; 20:196-206. [PMID: 20167475 DOI: 10.1016/j.sbi.2010.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 01/19/2023]
Abstract
In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
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32
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Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell Mol Life Sci 2010; 67:255-76. [PMID: 19851829 PMCID: PMC11115962 DOI: 10.1007/s00018-009-0164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/14/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.
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Affiliation(s)
- Andrew I. Jewett
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
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Overexpression of the groESL operon enhances the heat and salinity stress tolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC7120. Appl Environ Microbiol 2009; 75:6008-12. [PMID: 19633117 DOI: 10.1128/aem.00838-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The bicistronic groESL operon, encoding the Hsp60 and Hsp10 chaperonins, was cloned into an integrative expression vector, pFPN, and incorporated at an innocuous site in the Anabaena sp. strain PCC7120 genome. In the recombinant Anabaena strain, the additional groESL operon was expressed from a strong cyanobacterial P(psbA1) promoter without hampering the stress-responsive expression of the native groESL operon. The net expression of the two groESL operons promoted better growth, supported the vital activities of nitrogen fixation and photosynthesis at ambient conditions, and enhanced the tolerance of the recombinant Anabaena strain to heat and salinity stresses.
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Powers ET, Morimoto RI, Dillin A, Kelly JW, Balch WE. Biological and chemical approaches to diseases of proteostasis deficiency. Annu Rev Biochem 2009; 78:959-91. [PMID: 19298183 DOI: 10.1146/annurev.biochem.052308.114844] [Citation(s) in RCA: 840] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many diseases appear to be caused by the misregulation of protein maintenance. Such diseases of protein homeostasis, or "proteostasis," include loss-of-function diseases (cystic fibrosis) and gain-of-toxic-function diseases (Alzheimer's, Parkinson's, and Huntington's disease). Proteostasis is maintained by the proteostasis network, which comprises pathways that control protein synthesis, folding, trafficking, aggregation, disaggregation, and degradation. The decreased ability of the proteostasis network to cope with inherited misfolding-prone proteins, aging, and/or metabolic/environmental stress appears to trigger or exacerbate proteostasis diseases. Herein, we review recent evidence supporting the principle that proteostasis is influenced both by an adjustable proteostasis network capacity and protein folding energetics, which together determine the balance between folding efficiency, misfolding, protein degradation, and aggregation. We review how small molecules can enhance proteostasis by binding to and stabilizing specific proteins (pharmacologic chaperones) or by increasing the proteostasis network capacity (proteostasis regulators). We propose that such therapeutic strategies, including combination therapies, represent a new approach for treating a range of diverse human maladies.
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Affiliation(s)
- Evan T Powers
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Abstract
Most proteins must fold into precise three-dimensional conformations to fulfill their biological functions. Here we review recent concepts emerging from studies of protein folding in vitro and in vivo, with a focus on how proteins navigate the complex folding energy landscape inside cells with the aid of molecular chaperones. Understanding these reactions is also of considerable medical relevance, as the aggregation of misfolding proteins that escape the cellular quality-control machinery underlies a range of debilitating diseases, including many age-onset neurodegenerative disorders.
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Horwich AL, Apetri AC, Fenton WA. The GroEL/GroES cis cavity as a passive anti-aggregation device. FEBS Lett 2009; 583:2654-62. [PMID: 19577567 PMCID: PMC2759771 DOI: 10.1016/j.febslet.2009.06.049] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/27/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
The GroEL/GroES chaperonin folding chamber is an encapsulated space of approximately 65 A diameter with a hydrophilic wall, inside of which many cellular proteins reach the native state. The question of whether the cavity wall actively directs folding reactions or is playing a passive role has been open. We review past and recent observations and conclude that the chamber functions as a passive "Anfinsen cage" that prevents folding monomers from multimolecular aggregation.
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Affiliation(s)
- Arthur L Horwich
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
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GroEL-assisted protein folding: does it occur within the chaperonin inner cavity? Int J Mol Sci 2009; 10:2066-2083. [PMID: 19564940 PMCID: PMC2695268 DOI: 10.3390/ijms10052066] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 05/08/2009] [Accepted: 05/11/2009] [Indexed: 11/22/2022] Open
Abstract
The folding of protein molecules in the GroEL inner cavity under the co-chaperonin GroES lid is widely accepted as a crucial event of GroEL-assisted protein folding. This review is focused on the data showing that GroEL-assisted protein folding may proceed out of the complex with the chaperonin. The models of GroEL-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the GroEL surface and their folding in the bulk solution are also discussed.
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38
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Select pyrimidinones inhibit the propagation of the malarial parasite, Plasmodium falciparum. Bioorg Med Chem 2009; 17:1527-33. [PMID: 19195901 DOI: 10.1016/j.bmc.2009.01.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 01/01/2009] [Accepted: 01/08/2009] [Indexed: 01/30/2023]
Abstract
Plasmodium falciparum, the Apicomplexan parasite that is responsible for the most lethal forms of human malaria, is exposed to radically different environments and stress factors during its complex lifecycle. In any organism, Hsp70 chaperones are typically associated with tolerance to stress. We therefore reasoned that inhibition of P. falciparum Hsp70 chaperones would adversely affect parasite homeostasis. To test this hypothesis, we measured whether pyrimidinone-amides, a new class of Hsp70 modulators, could inhibit the replication of the pathogenic P. falciparum stages in human red blood cells. Nine compounds with IC(50) values from 30 nM to 1.6 micrOM were identified. Each compound also altered the ATPase activity of purified P. falciparum Hsp70 in single-turnover assays, although higher concentrations of agents were required than was necessary to inhibit P. falciparum replication. Varying effects of these compounds on Hsp70s from other organisms were also observed. Together, our data indicate that pyrimidinone-amides constitute a novel class of anti-malarial agents.
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39
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Suzuki M, Ueno T, Iizuka R, Miura T, Zako T, Akahori R, Miyake T, Shimamoto N, Aoki M, Tanii T, Ohdomari I, Funatsu T. Effect of the C-terminal truncation on the functional cycle of chaperonin GroEL: implication that the C-terminal region facilitates the transition from the folding-arrested to the folding-competent state. J Biol Chem 2008; 283:23931-9. [PMID: 18583344 PMCID: PMC3259756 DOI: 10.1074/jbc.m804090200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 06/25/2008] [Indexed: 11/06/2022] Open
Abstract
To elucidate the exact role of the C-terminal region of GroEL in its functional cycle, the C-terminal 20-amino acid truncated mutant of GroEL was constructed. The steady-state ATPase rate and duration of GroES binding showed that the functional cycle of the truncated GroEL is extended by approximately 2 s in comparison with that of the wild type, without interfering with the basic functions of GroEL. We have proposed a model for the functional cycle of GroEL, which consists of two rate-limiting steps of approximately 3- and approximately 5-s duration (Ueno, T., Taguchi, H., Tadakuma, H., Yoshida, M., and Funatsu, T. (2004) Mol. Cell 14, 423-434 g). According to the model, detailed kinetic studies were performed. We found that a 20-residue truncation of the C terminus extends the time until inorganic phosphate is generated and the time for arresting protein folding in the central cavity, i.e. the lifetime of the first rate-limiting step in the functional cycle, to an approximately 5-s duration. These results suggest that the integrity of the C-terminal region facilitates the transition from the first to the second rate-limiting state.
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Affiliation(s)
- Mihoko Suzuki
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taro Ueno
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryo Iizuka
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takahiro Miura
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tamotsu Zako
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rena Akahori
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Miyake
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naonobu Shimamoto
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mutsuko Aoki
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Tanii
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Iwao Ohdomari
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Funatsu
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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