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A general approach to protein folding using thermostable exoshells. Nat Commun 2021; 12:5720. [PMID: 34588451 PMCID: PMC8481291 DOI: 10.1038/s41467-021-25996-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
In vitro protein folding is a complex process which often results in protein aggregation, low yields and low specific activity. Here we report the use of nanoscale exoshells (tES) to provide complementary nanoenvironments for the folding and release of 12 highly diverse protein substrates ranging from small protein toxins to human albumin, a dimeric protein (alkaline phosphatase), a trimeric ion channel (Omp2a) and the tetrameric tumor suppressor, p53. These proteins represent a unique diversity in size, volume, disulfide linkages, isoelectric point and multi versus monomeric nature of their functional units. Protein encapsulation within tES increased crude soluble yield (3-fold to >100-fold), functional yield (2-fold to >100-fold) and specific activity (3-fold to >100-fold) for all the proteins tested. The average soluble yield was 6.5 mg/100 mg of tES with charge complementation between the tES internal cavity and the protein substrate being the primary determinant of functional folding. Our results confirm the importance of nanoscale electrostatic effects and provide a solution for folding proteins in vitro.
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2
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Ma X, Feng Y. Hypercholesterolemia Tunes Hematopoietic Stem/Progenitor Cells for Inflammation and Atherosclerosis. Int J Mol Sci 2016; 17:E1162. [PMID: 27447612 PMCID: PMC4964534 DOI: 10.3390/ijms17071162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 12/17/2022] Open
Abstract
As the pathological basis of cardiovascular disease (CVD), atherosclerosis is featured as a chronic inflammation. Hypercholesterolemia is an independent risk factor for CVD. Accumulated studies have shown that hypercholesterolemia is associated with myeloid cell expansion, which stimulates innate and adaptive immune responses, strengthens inflammation, and accelerates atherosclerosis progression. Hematopoietic stem/progenitor cells (HSPC) in bone marrow (BM) expresses a panel of lipoprotein receptors to control cholesterol homeostasis. Deficiency of these receptors abrogates cellular cholesterol efflux, resulting in HSPC proliferation and differentiation in hypercholesterolemic mice. Reduction of the cholesterol level in the lipid rafts by infusion of reconstituted high-density lipoprotein (HDL) or its major apolipoprotein, apoA-I, reverses hypercholesterolemia-induced HSPC expansion. Apart from impaired cholesterol metabolism, inhibition of reactive oxygen species production suppresses HSPC activation and leukocytosis. These data indicate that the mechanisms underlying the effects of hypercholesterolemia on HSPC proliferation and differentiation could be multifaceted. Furthermore, dyslipidemia also regulates HSPC-neighboring cells, resulting in HSPC mobilization. In the article, we review how hypercholesterolemia evokes HSPC activation and mobilization directly or via its modification of BM microenvironment. We hope this review will bring light to finding key molecules to control HSPC expansion, inflammation, and atherosclerosis for the treatment of CVD.
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Affiliation(s)
- Xiaojuan Ma
- Beijing Key Laboratory of Diabetes Prevention and Research, Lu He Hospital, Capital Medical University, Beijing 101149, China.
- Department of Endocrinology, Lu He Hospital, Capital Medical University, Beijing 101149, China.
| | - Yingmei Feng
- Beijing Key Laboratory of Diabetes Prevention and Research, Lu He Hospital, Capital Medical University, Beijing 101149, China.
- Department of Endocrinology, Lu He Hospital, Capital Medical University, Beijing 101149, China.
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3
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Co NT, Hu CK, Li MS. Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models. J Chem Phys 2013; 138:185101. [PMID: 23676073 DOI: 10.1063/1.4804299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We have developed the lattice model for describing polypeptide chains in the presence of crowders. The influence of crowding confinement on the fibrillation kinetics of polypeptide chains is studied using this model. We observed the non-trivial behavior of the fibril formation time τfib that it decreases with the concentration of crowders if crowder sizes are large enough, but the growth is observed for crowders of small sizes. This allows us to explain the recent experimental observation on the dual effect of crowding particles on fibril growth of proteins that for a fixed crowder concentration the fibrillation kinetics is fastest at intermediate values of total surface of crowders. It becomes slow at either small or large coverages of cosolutes. It is shown that due to competition between the energetics and entropic effects, the dependence of τfib on the size of confined space is described by a parabolic function.
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Affiliation(s)
- Nguyen Truong Co
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
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Zhang K, Wang L, Liu Y, Chan KY, Pang X, Schulten K, Dong Z, Sun F. Flexible interwoven termini determine the thermal stability of thermosomes. Protein Cell 2013; 4:432-44. [PMID: 23709365 DOI: 10.1007/s13238-013-3026-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 04/26/2013] [Indexed: 01/27/2023] Open
Abstract
Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II chaperonin assembly and thermal stability is yet to be elucidated. Here, we selected the group II chaperonins (cpn-α and cpn-β), also called thermosomes, from Acidianus tengchongensis and investigated their assembly and thermal stability. We found that the binding of ATP or its analogs contributed to the successful assembly of thermosomes and enhanced their thermal stabilities. Cpn-β is more thermally stable than cpn-α, while the thermal stability of the hetero thermosome cpn-αβ is intermediate. Cryo-electron microscopy reconstructions of cpn-α and cpn-β revealed the interwoven densities of their non-conserved flexible N/C-termini around the equatorial planes. The deletion or swapping of their termini and pH-dependent thermal stability assays revealed the key role of the termini electrostatic interactions in the assembly and thermal stability of the thermosomes.
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Affiliation(s)
- Kai Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Priya S, Sharma SK, Goloubinoff P. Molecular chaperones as enzymes that catalytically unfold misfolded polypeptides. FEBS Lett 2013; 587:1981-7. [PMID: 23684649 DOI: 10.1016/j.febslet.2013.05.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Stress-denatured or de novo synthesized and translocated unfolded polypeptides can spontaneously reach their native state without assistance of other proteins. Yet, the pathway to native folding is complex, stress-sensitive and prone to errors. Toxic misfolded and aggregated conformers may accumulate in cells and lead to degenerative diseases. Members of the canonical conserved families of molecular chaperones, Hsp100s, Hsp70/110/40s, Hsp60/CCTs, the small Hsps and probably also Hsp90s, can recognize and bind with high affinity, abnormally exposed hydrophobic surfaces on misfolded and aggregated polypeptides. Binding to Hsp100, Hsp70, Hsp110, Hsp40, Hsp60, CCTs and Trigger factor may cause partial unfolding of the misfolded polypeptide substrates, and ATP hydrolysis can induce further unfolding and release from the chaperone, leading to spontaneous refolding into native proteins with low-affinity for the chaperones. Hence, specific chaperones act as catalytic polypeptide unfolding isomerases, rerouting cytotoxic misfolded and aggregated polypeptides back onto their physiological native refolding pathway, thus averting the onset of protein conformational diseases.
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Affiliation(s)
- Smriti Priya
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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Raran-Kurussi S, Waugh DS. The ability to enhance the solubility of its fusion partners is an intrinsic property of maltose-binding protein but their folding is either spontaneous or chaperone-mediated. PLoS One 2012; 7:e49589. [PMID: 23166722 PMCID: PMC3500312 DOI: 10.1371/journal.pone.0049589] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli maltose binding protein (MBP) is commonly used to promote the solubility of its fusion partners. To investigate the mechanism of solubility enhancement by MBP, we compared the properties of MBP fusion proteins refolded in vitro with those of the corresponding fusion proteins purified under native conditions. We fused five aggregation-prone passenger proteins to 3 different N-terminal tags: His6-MBP, His6-GST and His6. After purifying the 15 fusion proteins under denaturing conditions and refolding them by rapid dilution, we recovered far more of the soluble MBP fusion proteins than their GST- or His-tagged counterparts. Hence, we can reproduce the solubilizing activity of MBP in a simple in vitro system, indicating that no additional factors are required to mediate this effect. We assayed both the soluble fusion proteins and their TEV protease digestion products (i.e., with the N-terminal tag removed) for biological activity. Little or no activity was detected for some fusion proteins whereas others were quite active. When the MBP fusions proteins were purified from E. coli under native conditions they were all substantially active. These results indicate that the ability of MBP to promote the solubility of its fusion partners in vitro sometimes, but not always, results in their proper folding. We show that the folding of some passenger proteins is mediated by endogenous chaperones in vivo. Hence, MBP serves as a passive participant in the folding process; passenger proteins either fold spontaneously or with the assistance of chaperones.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David S. Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
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Anisimov VM, Bliznyuk AA. Charge Transfer Effects in the GroEL–GroES Chaperonin Tetramer in Solution. J Phys Chem B 2012; 116:6261-8. [DOI: 10.1021/jp211385e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor M. Anisimov
- National Center for Supercomputing
Applications, University of Illinois at Urbana—Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Andrey A. Bliznyuk
- Australian National University, Supercomputer Facility, Leonard Huxley Bld.
(#56), Canberra, ACT 0200, Australia
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8
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Abstract
The central dogma of molecular biology - DNA makes RNA makes proteins - is a flow of information that in eukaryotes encounters a physical barrier: the nuclear envelope, which encapsulates, organizes and protects the genome. Nuclear-pore complexes, embedded in the nuclear envelope, regulate the passage of molecules to and from the nucleus, including the poorly understood process of the export of RNAs from the nucleus. Recent imaging approaches focusing on single molecules have provided unexpected insight into this crucial step in the information flow. This review addresses the latest studies of RNA export and presents some models for how this complex process may work.
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Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome: a systems approach. Comp Funct Genomics 2010:254836. [PMID: 18464924 PMCID: PMC2367384 DOI: 10.1155/2008/254836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 02/19/2008] [Indexed: 12/04/2022] Open
Abstract
To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved 53% proteome coverage. To study the differential protein expression in response to sub-MIC antibiotics in the context of protein interaction networks, we inferred P. multocida Pm70 protein interaction network from orthologous proteins. We then overlaid the differential protein expression data onto the P. multocida protein interaction network to study the bacterial response. We identified proteins that could enhance antimicrobial activity. Overall compensatory response to antibiotics was characterized by altered expression of proteins involved in purine metabolism, stress response, and cell envelope permeability.
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Wang L, Hu ZJ, Luo YM, Huo YW, Ma Q, He YZ, Zhang YY, Sun F, Dong ZY. Distinct symmetry and limited peptide refolding activity of the thermosomes from the acidothermophilic archaea Acidianus tengchongensis S5(T). Biochem Biophys Res Commun 2010; 393:228-34. [PMID: 20117082 DOI: 10.1016/j.bbrc.2010.01.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 01/27/2010] [Indexed: 11/28/2022]
Abstract
Recombinant thermosomes from the Acidianus tengchongensis strain S5(T) were purified to homogeneity and assembled in vitro into homo-oligomers (rATcpnalpha or rATcpnbeta) and hetero-oligomers (rATcpnalphabeta). The symmetries of these complexes were determined by electron microscopy and image analysis. The rATcpnalpha homo-oligomer was shown to possess 8-fold symmetry while both rATcpnbeta and rATcpnalphabeta oligomers adopted 9-fold symmetry. rATcpnalphabeta oligomers were shown to contain the alpha and beta subunits in a 1:2 ratio. All of the complexes prevented the irreversible inactivation of yeast alcohol dehydrogenase at 55 degrees C and completely prevented the formation of aggregates during thermal inactivation of citrate synthase at 45 degrees C. All rATcpn complexes showed trace ATP hydrolysis activity. Furthermore, rATcpnbeta sequestered fully chemically denatured substrates (GFP and thermophilic malic dehydrogenase) in vitro without refolding them in an ATP-dependent manner. This property is similar to previously reported properties of chaperonins from Sulfolobus tokodaii and Sulfolobus acidocaldarius. These features are consistent with the slow growth rates of these species of archaea in their native environment.
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Affiliation(s)
- Li Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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Chow AM, Ferrier-Pagès C, Khalouei S, Reynaud S, Brown IR. Increased light intensity induces heat shock protein Hsp60 in coral species. Cell Stress Chaperones 2009; 14:469-76. [PMID: 19214783 PMCID: PMC2728280 DOI: 10.1007/s12192-009-0100-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 01/15/2009] [Accepted: 01/19/2009] [Indexed: 10/21/2022] Open
Abstract
The effect of increased light intensity and heat stress on heat shock protein Hsp60 was examined in two coral species using a branched coral and a laminar coral, selected for their different resistance to environmental perturbation. Transient Hsp60 induction was observed in the laminar coral following either light or thermal stress. Sustained induction was observed when these stresses were combined. The branched coral exhibited comparatively weak transient Hsp60 induction after heat stress and no detectable induction following light stress, consistent with its susceptibility to bleaching in native environments compared to the laminar coral. Our observations also demonstrate that increased light intensity and heat stress exhibited a greater negative impact on the photosynthetic capacity of environmentally sensitive branched coral than the more resistant laminar coral. This supports a correlation between stress induction of Hsp60 and (a) ability to counter perturbation of photosynthetic capacity by light and heat stress and (b) resistance to environmentally induced coral bleaching.
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Affiliation(s)
- Ari M. Chow
- Department of Biological Sciences, University of Toronto at Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada
| | | | - Sam Khalouei
- Department of Biological Sciences, University of Toronto at Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada
| | | | - Ian R. Brown
- Department of Biological Sciences, University of Toronto at Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada
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Dong C, Shao L, Guo J, Ren J. Host-Guest Interaction of Chaperonin GroEL and Water-Soluble CdTe Quantum Dots and its Size-Selective Inclusion. Chemphyschem 2008; 9:2245-51. [DOI: 10.1002/cphc.200800398] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis: the major cytosolic and membrane proteins. Arch Microbiol 2008; 190:379-94. [PMID: 18584152 PMCID: PMC2755778 DOI: 10.1007/s00203-008-0399-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 05/21/2008] [Accepted: 06/09/2008] [Indexed: 12/25/2022]
Abstract
Ignicoccus hospitalis, a hyperthermophilic, chemolithoautotrophic Crenarchaeon, is the host of Nanoarchaeum equitans. Together, they form an intimate association, the first among Archaea. Membranes are of fundamental importance for the interaction of I. hospitalis and N. equitans, as they harbour the proteins necessary for the transport of macromolecules like lipids, amino acids, and cofactors between these organisms. Here, we investigated the protein inventory of I. hospitalis cells, and were able to identify 20 proteins in total. Experimental evidence and predictions let us conclude that 11 are soluble cytosolic proteins, eight membrane or membrane-associated proteins, and a single one extracellular. The quantitatively dominating proteins in the cytoplasm (peroxiredoxin; thermosome) antagonize oxidative and temperature stress which I. hospitalis cells are exposed to at optimal growth conditions. Three abundant membrane protein complexes are found: the major protein of the outer membrane, which might protect the cell against the hostile environment, forms oligomeric complexes with pores of unknown selectivity; two other complexes of the cytoplasmic membrane, the hydrogenase and the ATP synthase, play a key role in energy production and conversion.
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Hu M, Wang J, Peng Q. Identification and visualization of cage-shaped proteins. Bioinformatics 2007; 23:3400-2. [DOI: 10.1093/bioinformatics/btm476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Marenduzzo D, Finan K, Cook PR. The depletion attraction: an underappreciated force driving cellular organization. ACTA ACUST UNITED AC 2007; 175:681-6. [PMID: 17145959 PMCID: PMC2064666 DOI: 10.1083/jcb.200609066] [Citation(s) in RCA: 257] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force—the “depletion attraction”—also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.
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Affiliation(s)
- Davide Marenduzzo
- School of Physics, University of Edinburgh, Edinburgh, EH9 3JZ, Scotland, UK
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