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Zhou L, Sheng B, Zhang T, Liu W, Guo K, Yu H, Bai L, Hu J. madd-4 plays a critical role in light against Bursaphelenchus xylophilus. Sci Rep 2022; 12:14796. [PMID: 36042283 PMCID: PMC9427778 DOI: 10.1038/s41598-022-19263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022] Open
Abstract
Bursaphelenchus xylophilus is a notorious invasive species, causing extensive losses to pine ecosystems globally. Previous studies had shown that the development of B. xylophilus was seriously suppressed by light. However, the mechanism involved in the inhibition is unknown. Here, it is the first report that Bxy-madd-4 is a light-regulated gene, plays a potential role in B. xylophilus in responding to the blue light. Transcriptome sequencing revealed that the expression level of Bxy-madd-4 declined by 86.39% under blue light. The reverse transcription quantitative real-time PCR results were in accord with the transcriptome sequencing, confirming the expression level of Bxy-madd-4 was suppressed by blue light. Bxy-madd-4 promoter::mCherry reporter constructed in Caenorhabditis elegans were utilized to mimic the spatiotemporal expression patterns of Bxy-madd-4. Bxy-madd-4A promoter activity had a strong continuity throughout all development stages in C. elegans. Further RNA interference indicated that only 36.8% of the Bxy-madd-4 dsRNA treated embryos were hatched. Moreover, 71.6% of the hatched nematodes were abnormal, such as particles on the body surface and concave tissues. Our findings contribute towards a better understanding of the mechanism of light against the destructive invasive nematode, providing a promising hint for control of the destructive invasive nematode.
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Affiliation(s)
- Lifeng Zhou
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Bicheng Sheng
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Tianyuan Zhang
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Wenyi Liu
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Kai Guo
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hongshi Yu
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Liqun Bai
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Jiafu Hu
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
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2
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Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A 2022; 119:2109169119. [PMID: 34969836 PMCID: PMC8740594 DOI: 10.1073/pnas.2109169119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022] Open
Abstract
Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli's lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.
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3
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Lee HC, Binos S, Chapman K, Pulsford SB, Ivanovici A, Rathjen JP, Djordjevic MA. A new method to visualize CEP hormone-CEP receptor interactions in vascular tissue in vivo. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6164-6174. [PMID: 34059899 DOI: 10.1093/jxb/erab244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
C-TERMINALLY ENCODED PEPTIDEs (CEPs) control diverse responses in plants including root development, root system architecture, nitrogen demand signalling, and nutrient allocation that influences yield, and there is evidence that different ligands impart different phenotypic responses. Thus, there is a need for a simple method that identifies bona fide CEP hormone-receptor pairings in vivo and examines whether different CEP family peptides bind the same receptor. We used formaldehyde or photoactivation to cross-link fluorescently tagged group 1 or group 2 CEPs to receptors in semi-purified Medicago truncatula or Arabidopsis thaliana leaf vascular tissues to verify that COMPACT ROOT ARCHITECTURE 2 (CRA2) is the Medicago CEP receptor, and to investigate whether sequence diversity within the CEP family influences receptor binding. Formaldehyde cross-linked the fluorescein isothiocyanate (FITC)-tagged Medicago group 1 CEP (MtCEP1) to wild-type Medicago or Arabidopsis vascular tissue cells, but not to the CEP receptor mutants, cra2 or cepr1. Binding competition showed that unlabelled MtCEP1 displaces FITC-MtCEP1 from CRA2. In contrast, the group 2 CEP, FITC-AtCEP14, bound to vascular tissue independently of CEPR1 or CRA2, and AtCEP14 did not complete with FITC-MtCEP1 to bind CEP receptors. The binding of a photoactivatable FITC-MtCEP1 to the periphery of Medicago vascular cells suggested that CRA2 localizes to the plasma membrane. We separated and visualized a fluorescent 105 kDa protein corresponding to the photo-cross-linked FITC-MtCEP1-CRA2 complex using SDS-PAGE. Mass spectrometry identified CRA2-specific peptides in this protein band. The results indicate that FITC-MtCEP1 binds to CRA2, MtCRA2 and AtCEPR1 are functionally equivalent, and the binding specificities of group 1 and group 2 CEPs are distinct. Using formaldehyde or photoactivated cross-linking of biologically active, fluorescently tagged ligands may find wider utility by identifying CEP-CEP receptor pairings in diverse plants.
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Affiliation(s)
- Han-Chung Lee
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Steve Binos
- Thermo Fisher Scientific, Bio21 Institute, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kelly Chapman
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Sacha B Pulsford
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - John P Rathjen
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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4
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Winogradoff D, John S, Aksimentiev A. Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly. NANOSCALE 2020; 12:5422-5434. [PMID: 32080694 PMCID: PMC7291819 DOI: 10.1039/c9nr09135a] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein-SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins-I27 domain of titin and β-amylase-obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein's secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS-protein interactions sets the stage for future refinement of SDS-enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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5
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Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D. Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II. J Mol Biol 2018; 430:4068-4086. [PMID: 30098339 DOI: 10.1016/j.jmb.2018.07.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Our understanding on the folding of membrane proteins lags behind that of soluble proteins due to challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding pathways, we have systematically investigated the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 ΧSDS), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal-binding pocket is disrupted, with transmembrane residues becoming more solvent exposed. Folding of pSRII from an SDS-denatured state harboring a covalently bound retinal chromophore shows deviations from an apparent two-state behavior. SDS denaturation to form the sensory opsin apo-protein is reversible. We report pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin.
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Affiliation(s)
- Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
| | - James Mitchell
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Judith Klein-Seetharaman
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom.
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6
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Honda N, Tsukamoto T, Sudo Y. Comparative evaluation of the stability of seven-transmembrane microbial rhodopsins to various physicochemical stimuli. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Krainer G, Gracia P, Frotscher E, Hartmann A, Gröger P, Keller S, Schlierf M. Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A. Biophys J 2017. [PMID: 28629619 DOI: 10.1016/j.bpj.2017.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds. We find that even under strongly denaturing conditions and in the absence of residual secondary structure, OmpLA populates an ensemble of slowly (>100 ms) interconverting and conformationally heterogeneous unfolded states that lack the fast chain-reconfiguration motions expected for an unstructured, fully unfolded chain. The drastically slowed sampling of potentially folding-competent states, as compared with a random-coil polypeptide, may contribute to the slow in vitro folding kinetics observed for many OMPs. In vivo, however, slow intramolecular long-range dynamics might be advantageous for entropically favored binding of unfolded OMPs to chaperones and, by facilitating conformational selection after release from chaperones, for preserving binding-competent conformations before insertion into the outer membrane.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany; Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pablo Gracia
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Erik Frotscher
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Philip Gröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany.
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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8
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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9
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Gong J, Yuan Y, Ward A, Kang L, Zhang B, Wu Z, Peng J, Feng Z, Liu J, Xu XZS. The C. elegans Taste Receptor Homolog LITE-1 Is a Photoreceptor. Cell 2016; 167:1252-1263.e10. [PMID: 27863243 PMCID: PMC5388352 DOI: 10.1016/j.cell.2016.10.053] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 09/05/2016] [Accepted: 10/28/2016] [Indexed: 01/20/2023]
Abstract
Many animal tissues/cells are photosensitive, yet only two types of photoreceptors (i.e., opsins and cryptochromes) have been discovered in metazoans. The question arises as to whether unknown types of photoreceptors exist in the animal kingdom. LITE-1, a seven-transmembrane gustatory receptor (GR) homolog, mediates UV-light-induced avoidance behavior in C. elegans. However, it is not known whether LITE-1 functions as a chemoreceptor or photoreceptor. Here, we show that LITE-1 directly absorbs both UVA and UVB light with an extinction coefficient 10-100 times that of opsins and cryptochromes, indicating that LITE-1 is highly efficient in capturing photons. Unlike typical photoreceptors employing a prosthetic chromophore to capture photons, LITE-1 strictly depends on its protein conformation for photon absorption. We have further identified two tryptophan residues critical for LITE-1 function. Interestingly, unlike GPCRs, LITE-1 adopts a reversed membrane topology. Thus, LITE-1, a taste receptor homolog, represents a distinct type of photoreceptor in the animal kingdom.
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Affiliation(s)
- Jianke Gong
- College of Life Science and Technology, Collaborative Innovation Center for Brain Science, and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yiyuan Yuan
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alex Ward
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Kang
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bi Zhang
- College of Life Science and Technology, Collaborative Innovation Center for Brain Science, and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zhaoyang Feng
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jianfeng Liu
- College of Life Science and Technology, Collaborative Innovation Center for Brain Science, and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - X Z Shawn Xu
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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10
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Chi H, Wang X, Li J, Ren H, Huang F. Chaperonin-enhanced Escherichia coli cell-free expression of functional CXCR4. J Biotechnol 2016; 231:193-200. [PMID: 27316829 DOI: 10.1016/j.jbiotec.2016.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/23/2016] [Accepted: 06/13/2016] [Indexed: 11/15/2022]
Abstract
G protein-coupled receptors (GPCRs) are important therapeutic targets for a broad spectrum of diseases and disorders. Obtaining milligram quantities of functional receptors through the development of robust production methods are highly demanded to probe GPCR structure and functions. In this study, we analyzed synergies of the bacterial chaperonin GroEL-GroES and cell-free expression for the production of functionally folded C-X-C chemokine GPCR type 4 (CXCR4). The yield of soluble CXCR4 in the presence of detergent Brij-35 reached ∼1.1mg/ml. The chaperonin complex added was found to significantly enhance the productive folding of newly synthesized CXCR4, by increasing both the rate (∼30-fold) and the yield (∼1.3-fold) of folding over its spontaneous behavior. Meanwhile, the structural stability of CXCR4 was also improved with supplied GroEL-GroES, as was the soluble expression of biologically active CXCR4 with a ∼1.4-fold increase. The improved stability together with the higher ligand binding affinity suggests more efficient folding. The essential chaperonin GroEL was shown to be partially effective on its own, but for maximum efficiency both GroEL and its co-chaperonin GroES were necessary. The method reported here should prove generally useful for cell-free production of large amounts of natively folded GPCRs, and even other classes of membrane proteins.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China; College of Science, China University of Petroleum (East China), Qingdao 266580, PR China.
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
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11
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Volz P, Krause N, Balke J, Schneider C, Walter M, Schneider F, Schlesinger R, Alexiev U. Light and pH-induced Changes in Structure and Accessibility of Transmembrane Helix B and Its Immediate Environment in Channelrhodopsin-2. J Biol Chem 2016; 291:17382-93. [PMID: 27268055 DOI: 10.1074/jbc.m115.711200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Indexed: 11/06/2022] Open
Abstract
A variant of the cation channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) was selectively labeled at position Cys-79 at the end of the first cytoplasmic loop and the beginning of transmembrane helix B with the fluorescent dye fluorescein (acetamidofluorescein). We utilized (i) time-resolved fluorescence anisotropy experiments to monitor the structural dynamics at the cytoplasmic surface close to the inner gate in the dark and after illumination in the open channel state and (ii) time-resolved fluorescence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4. The light-induced increase in final anisotropy for acetamidofluorescein bound to the channel variant with a prolonged conducting state clearly shows that the formation of the open channel state is associated with a large conformational change at the cytoplasmic surface, consistent with an outward tilt of helix B. Furthermore, results from solute accessibility studies of the cytoplasmic end of helix B suggest a pH-dependent structural heterogeneity that appears below pH 7. At pH 7.4 conformational homogeneity was observed, whereas at pH 6.0 two protein fractions exist, including one in which residue 79 is buried. This inaccessible fraction amounts to 66% in nanodiscs and 82% in micelles. Knowledge about pH-dependent structural heterogeneity may be important for CrChR2 applications in optogenetics.
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Affiliation(s)
- Pierre Volz
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Nils Krause
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Jens Balke
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Constantin Schneider
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Maria Walter
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Franziska Schneider
- the Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Ramona Schlesinger
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
| | - Ulrike Alexiev
- From the Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany and
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12
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Guo R, Gaffney K, Yang Z, Kim M, Sungsuwan S, Huang X, Hubbell WL, Hong H. Steric trapping reveals a cooperativity network in the intramembrane protease GlpG. Nat Chem Biol 2016; 12:353-360. [PMID: 26999782 PMCID: PMC4837050 DOI: 10.1038/nchembio.2048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 01/22/2016] [Indexed: 12/21/2022]
Abstract
Membrane proteins are assembled through balanced interactions among protein, lipids and water. Studying their folding while maintaining the native lipid environment is necessary but challenging. Here we present methods for analyzing key elements in membrane protein folding including thermodynamic stability, compactness of the unfolded state and folding cooperativity under native conditions. The methods are based on steric trapping which couples unfolding of a doubly-biotinylated protein to binding of monovalent streptavidin (mSA). We further advanced this technology for general application by developing versatile biotin probes possessing spectroscopic reporters that are sensitized by mSA binding or protein unfolding. By applying these methods to an intramembrane protease GlpG of Escherichia coli, we elucidated a widely unraveled unfolded state, subglobal unfolding of the region encompassing the active site, and a network of cooperative and localized interactions to maintain the stability. These findings provide crucial insights into the folding energy landscape of membrane proteins.
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Affiliation(s)
- Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kristen Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Miyeon Kim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Suttipun Sungsuwan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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13
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Chi H, Wang X, Li J, Ren H, Huang F. Folding of newly translated membrane protein CCR5 is assisted by the chaperonin GroEL-GroES. Sci Rep 2015; 5:17037. [PMID: 26585937 PMCID: PMC4653635 DOI: 10.1038/srep17037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/23/2015] [Indexed: 01/20/2023] Open
Abstract
The in vitro folding of newly translated human CC chemokine receptor type 5
(CCR5), which belongs to the physiologically important family of G protein-coupled
receptors (GPCRs), has been studied in a cell-free system supplemented with the
surfactant Brij-35. The freshly synthesized CCR5 can spontaneously fold into its
biologically active state but only slowly and inefficiently. However, on addition of
the GroEL-GroES molecular chaperone system, the folding of the nascent CCR5 was
significantly enhanced, as was the structural stability and functional expression of
the soluble form of CCR5. The chaperonin GroEL was partially effective on its own,
but for maximum efficiency both the GroEL and its GroES lid were necessary. These
results are direct evidence for chaperone-assisted membrane protein folding and
therefore demonstrate that GroEL-GroES may be implicated in the folding of membrane
proteins.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
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14
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SDS-induced Peptide Conformational Changes: From Triglycyl-glycine to Amyloid-β Oligomers Associated with Alzheimer’s Disease. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9483-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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15
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Struts AV, Barmasov AV, Brown MF. SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. I. VIBRATIONAL AND ELECTRONIC SPECTROSCOPY. OPTICS AND SPECTROSCOPY 2015; 118:711-717. [PMID: 28260815 PMCID: PMC5334778 DOI: 10.1134/s0030400x15050240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance, NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- University of Arizona, Tucson, AZ 85721 USA
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16
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Witting M, Boreham A, Brodwolf R, Vávrová K, Alexiev U, Friess W, Hedtrich S. Interactions of hyaluronic Acid with the skin and implications for the dermal delivery of biomacromolecules. Mol Pharm 2015; 12:1391-401. [PMID: 25871518 DOI: 10.1021/mp500676e] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hyaluronic acid (HA) hydrogels are interesting delivery systems for topical applications. Besides moisturizing the skin and improving wound healing, HA facilitates topical drug absorption and is highly compatible with labile biomacromolecules. Hence, in this study we investigated the influence of HA hydrogels with different molecular weights (5 kDa, 100 kDa, 1 MDa) on the skin absorption of the model protein bovine serum albumin (BSA) using fluorescence lifetime imaging microscopy (FLIM). To elucidate the interactions of HA with the stratum corneum and the skin absorption of HA itself, we combined FLIM and Fourier-transform infrared (FTIR) spectroscopy. Our results revealed distinct formulation and skin-dependent effects. In barrier deficient (tape-stripped) skin, BSA alone penetrated into dermal layers. When BSA and HA were applied together, however, penetration was restricted to the epidermis. In normal skin, penetration enhancement of BSA into the epidermis was observed when applying low molecular weight HA (5 kDa). Fluorescence resonance energy transfer analysis indicated close interactions between HA and BSA under these conditions. FTIR spectroscopic analysis of HA interactions with stratum corneum constituents showed an α-helix to β-sheet interconversion of keratin in the stratum corneum, increased skin hydration, and intense interactions between 100 kDa HA and the skin lipids resulting in a more disordered arrangement of the latter. In conclusion, HA hydrogels restricted the delivery of biomacromolecules to the stratum corneum and viable epidermis in barrier deficient skin, and therefore seem to be potential topical drug vehicles. In contrast, HA acted as an enhancer for delivery in normal skin, probably mediated by a combination of cotransport, increased skin hydration, and modifications of the stratum corneum properties.
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Affiliation(s)
- Madeleine Witting
- †Department of Pharmaceutical Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Alexander Boreham
- ‡Department of Physics, Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
| | - Robert Brodwolf
- ‡Department of Physics, Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
| | - Kateřina Vávrová
- §Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University in Prague, Hradec Kralove, Czech Republic
| | - Ulrike Alexiev
- ‡Department of Physics, Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
| | - Wolfgang Friess
- †Department of Pharmaceutical Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sarah Hedtrich
- †Department of Pharmaceutical Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,∥Institute for Pharmaceutical Sciences, Freie Universität Berlin, Berlin, Germany
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17
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G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent. Biosci Rep 2015; 35:BSR20140171. [PMID: 25720391 PMCID: PMC4400634 DOI: 10.1042/bsr20140171] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins and are a major drug target. A serious obstacle to studying GPCR structure/function characteristics is the requirement to extract the receptors from their native environment in the plasma membrane, coupled with the inherent instability of GPCRs in the detergents required for their solubilization. In the present study, we report the first solubilization and purification of a functional GPCR [human adenosine A2A receptor (A2AR)], in the total absence of detergent at any stage, by exploiting spontaneous encapsulation by styrene maleic acid (SMA) co-polymer direct from the membrane into a nanoscale SMA lipid particle (SMALP). Furthermore, the A2AR–SMALP, generated from yeast (Pichia pastoris) or mammalian cells, exhibited increased thermostability (∼5°C) compared with detergent [DDM (n-dodecyl-β-D-maltopyranoside)]-solubilized A2AR controls. The A2AR–SMALP was also stable when stored for prolonged periods at 4°C and was resistant to multiple freeze-thaw cycles, in marked contrast with the detergent-solubilized receptor. These properties establish the potential for using GPCR–SMALP in receptor-based drug discovery assays. Moreover, in contrast with nanodiscs stabilized by scaffold proteins, the non-proteinaceous nature of the SMA polymer allowed unobscured biophysical characterization of the embedded receptor. Consequently, CD spectroscopy was used to relate changes in secondary structure to loss of ligand binding ([3H]ZM241385) capability. SMALP-solubilization of GPCRs, retaining the annular lipid environment, will enable a wide range of therapeutic targets to be prepared in native-like state to aid drug discovery and understanding of GPCR molecular mechanisms. It is universally acknowledged that exposing cell-surface receptors to detergent is detrimental. We have used a polymer to extract the receptor and surrounding lipid as a nanoparticle that provides a novel solution compatible with purification and receptor-based drug discovery assays.
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18
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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19
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The safety dance: biophysics of membrane protein folding and misfolding in a cellular context. Q Rev Biophys 2014; 48:1-34. [PMID: 25420508 DOI: 10.1017/s0033583514000110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Most biological processes require the production and degradation of proteins, a task that weighs heavily on the cell. Mutations that compromise the conformational stability of proteins place both specific and general burdens on cellular protein homeostasis (proteostasis) in ways that contribute to numerous diseases. Efforts to elucidate the chain of molecular events responsible for diseases of protein folding address one of the foremost challenges in biomedical science. However, relatively little is known about the processes by which mutations prompt the misfolding of α-helical membrane proteins, which rely on an intricate network of cellular machinery to acquire and maintain their functional structures within cellular membranes. In this review, we summarize the current understanding of the physical principles that guide membrane protein biogenesis and folding in the context of mammalian cells. Additionally, we explore how pathogenic mutations that influence biogenesis may differ from those that disrupt folding and assembly, as well as how this may relate to disease mechanisms and therapeutic intervention. These perspectives indicate an imperative for the use of information from structural, cellular, and biochemical studies of membrane proteins in the design of novel therapeutics and in personalized medicine.
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20
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Dutta A, Altenbach C, Mangahas S, Yanamala N, Gardner E, Hubbell WL, Klein-Seetharaman J. Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin. Biochemistry 2014; 53:7160-9. [PMID: 25268658 PMCID: PMC4245987 DOI: 10.1021/bi401557e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Rhodopsin
is a model system for understanding membrane protein
folding. Recently, conditions that allow maximally denaturing rhodopsin
without causing aggregation have been determined, opening the door
to the first structural characterization of denatured states of rhodopsin
by nuclear magnetic resonance (NMR) and electron paramagnetic resonance
(EPR) spectroscopy. One-dimensional 1H NMR spectra confirm
a progressive increase in flexibility of resonances in rhodopsin with
increasing denaturant concentrations. Two-dimensional 1H–15N HSQC spectra of [15N]-α-lysine-labeled
rhodopsin in which signals arise primarily from residues in the cytoplasmic
(CP) domain and of [15N]-α,ε-tryptophan-labeled
rhodopsin in which signals arise only from transmembrane (TM) and
extracellular (EC) residues indicate qualitatively that EC and CP
domains may be differentially affected by denaturation. To obtain
residue-specific information, particular residues in EC and CP domains
were investigated by site-directed spin labeling. EPR spectra of the
spin-labeled samples indicate that the EC residues retain more rigidity
in the denatured states than the CP residues. These results support
the notion of residual structure in denatured states of rhodopsin.
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Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
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21
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Boreham A, Brodwolf R, Pfaff M, Kim TY, Schlieter T, Mundhenk L, Gruber AD, Gröger D, Licha K, Haag R, Alexiev U. Temperature and environment dependent dynamic properties of a dendritic polyglycerol sulfate. POLYM ADVAN TECHNOL 2014. [DOI: 10.1002/pat.3355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alexander Boreham
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
| | - Robert Brodwolf
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine; Helmholtz-Zentrum Geesthacht; Teltow Germany
| | - Marcus Pfaff
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
- Faculty of Engineering and Computer Science; BTU Cottbus-Senftenberg; Großenhainer Str. 57 D-01968 Senftenberg Germany
| | - Tai-Yang Kim
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
| | - Thomas Schlieter
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
| | - Lars Mundhenk
- Institute of Veterinary Pathology; Freie Universität Berlin; Robert-von-Ostertag-Straße 15 D-14163 Berlin Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology; Freie Universität Berlin; Robert-von-Ostertag-Straße 15 D-14163 Berlin Germany
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine; Helmholtz-Zentrum Geesthacht; Teltow Germany
| | - Dominic Gröger
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustr. 3 D-14195 Berlin Germany
| | - Kai Licha
- mivenion GmbH; Robert-Koch-Platz 4 D-10115 Berlin Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustr. 3 D-14195 Berlin Germany
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine; Helmholtz-Zentrum Geesthacht; Teltow Germany
| | - Ulrike Alexiev
- Physics Department; Freie Universität Berlin; Arnimallee 14 D-14195 Berlin Germany
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine; Helmholtz-Zentrum Geesthacht; Teltow Germany
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22
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Kong X, Li Z, Lu D, Liu Z, Wu J. Multiscale simulation of surfactant–aquaporin complex formation and water permeability. RSC Adv 2014. [DOI: 10.1039/c4ra03759f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Molecular dynamics simulation reveals distinctive roles of electrostatic and hydrophobic interactions in surfactant (SDS)–protein (AqpZ) complex formation and functionality.
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Affiliation(s)
- Xian Kong
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
- Department of Chemical & Environmental Engineering
- University of California
| | - Zhixian Li
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Diannan Lu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Zheng Liu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Jianzhong Wu
- Department of Chemical & Environmental Engineering
- University of California
- Riverside, USA
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23
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Tastan O, Dutta A, Booth P, Klein-Seetharaman J. Retinal proteins as model systems for membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:656-63. [PMID: 24333783 DOI: 10.1016/j.bbabio.2013.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/19/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Abstract
Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks.
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Affiliation(s)
- Oznur Tastan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Arpana Dutta
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, USA
| | - Paula Booth
- School of Biochemistry, University of Bristol, UK
| | - Judith Klein-Seetharaman
- Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, UK.
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24
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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25
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Lee CR, Park YH, Kim YR, Peterkofsky A, Seok YJ. Phosphorylation-Dependent Mobility Shift of Proteins on SDS-PAGE is Due to Decreased Binding of SDS. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2063] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Roussel G, Tinti E, Perpète E, Michaux C. Refolding of SDS-denatured proteins using amphipathic cosolvents and osmolytes. ACTA ACUST UNITED AC 2013; Chapter 28:Unit28.5. [PMID: 23546624 DOI: 10.1002/0471140864.ps2805s72] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Currently, the investigation of protein refolding processes involves several time-consuming stages that require large amounts of protein and costly chemicals. Consequently, there is great interest in developing new approaches to the study of protein renaturation that are more technically and economically feasible. It has recently been reported that certain cosolvents are able to modulate the denaturing properties of sodium dodecyl sulfate (SDS) and induce the refolding of proteins. This unit presents a protocol to study and follow the renaturation of a protein (membrane or soluble) starting from a native or SDS-unfolded state using a variety of candidate cosolvents and osmolytes.
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Affiliation(s)
- Guillaume Roussel
- Department of Chemistry, Unité de Chimie Physique Théorique et Structurale, University of Namur, Namur, Belgium
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27
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Sychev SV, Barsukov LI, Ivanov VT. Conformation of gramicidin A in Triton X-100 micelles from CD and FTIR data: a clean example of antiparallel double β5.6 helix formation. J Pept Sci 2013; 19:452-8. [DOI: 10.1002/psc.2519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/09/2013] [Accepted: 04/19/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Leonid I. Barsukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
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28
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Schlebach JP, Peng D, Kroncke BM, Mittendorf KF, Narayan M, Carter BD, Sanders CR. Reversible folding of human peripheral myelin protein 22, a tetraspan membrane protein. Biochemistry 2013; 52:3229-41. [PMID: 23639031 DOI: 10.1021/bi301635f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Misfolding of the α-helical membrane protein peripheral myelin protein 22 (PMP22) has been implicated in the pathogenesis of the common neurodegenerative disease known as Charcot-Marie-Tooth disease (CMTD) and also several other related peripheral neuropathies. Emerging evidence suggests that the propensity of PMP22 to misfold in the cell may be due to an intrinsic lack of conformational stability. Therefore, quantitative studies of the conformational equilibrium of PMP22 are needed to gain insight into the molecular basis of CMTD. In this work, we have investigated the folding and unfolding of wild type (WT) human PMP22 in mixed micelles. Both kinetic and thermodynamic measurements demonstrate that the denaturation of PMP22 by n-lauroyl sarcosine (LS) in dodecylphosphocholine (DPC) micelles is reversible. Assessment of the conformational equilibrium indicates that a significant fraction of unfolded PMP22 persists even in the absence of the denaturing detergent. However, we find the stability of PMP22 is increased by glycerol, which facilitates quantitation of thermodynamic parameters. To our knowledge, this work represents the first report of reversible unfolding of a eukaryotic multispan membrane protein. The results indicate that WT PMP22 possesses minimal conformational stability in micelles, which parallels its poor folding efficiency in the endoplasmic reticulum. Folding equilibrium measurements for PMP22 in micelles may provide an approach to assess the effects of cellular metabolites or potential therapeutic agents on its stability. Furthermore, these results pave the way for future investigation of the effects of pathogenic mutations on the conformational equilibrium of PMP22.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Biochemistry and ‡Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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29
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Biswas S, Avan I, Basak AK, Abo-Dya NE, Asiri A, Katritzky AR. Photophysics of novel coumarin-labeled depsipeptides in solution: sensing interactions with SDS micelle via TICT model. Amino Acids 2013; 45:159-70. [PMID: 23553487 DOI: 10.1007/s00726-013-1483-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 02/23/2013] [Indexed: 12/12/2022]
Abstract
N-Acylbenzotriazoles enable the synthesis (69-92% yield) of blue to green fluorescent coumarin-labeled depsidipeptides 8a-f (quantum yields 0.004-0.97) and depsitripeptides 12a-d (quantum yields 0.02-0.96). Detailed photophysical studies of fluorescent coumarin-labeled depsipeptides 8a-f and 12a-d are reported for both polar protic and polar aprotic solvents. 7-Methoxy and 7-diethylaminocoumarin-3-ylcarbonyl depsipeptides 8c,f and 12d are highly solvent sensitive. These highly fluorescent compounds could be useful for peptide assays. Further photophysical studies of 7-diethylaminocoumarin-labeled depsipeptides 8c,12d within the micellar microenvironment of SDS reflect their ability to bind with the biological membrane, suggesting potential applications in the fields of bio- and medicinal chemistry.
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Affiliation(s)
- Suvendu Biswas
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL 32611-7200, USA
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30
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Roussel G, Perpète EA, Matagne A, Tinti E, Michaux C. Towards a universal method for protein refolding: The trimeric beta barrel membrane Omp2a as a test case. Biotechnol Bioeng 2012; 110:417-23. [DOI: 10.1002/bit.24722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/09/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
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31
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Astray G, Cid A, Manso J, Moldes O, Morales J, Quintás J. Dyes and biomimetic systems: detergency and food industry Colorantes y sistemas biomiméticos: detergencia e industria alimentaria. CYTA - JOURNAL OF FOOD 2011. [DOI: 10.1080/19476337.2011.585718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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32
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Veerappan A, Cymer F, Klein N, Schneider D. The Tetrameric α-Helical Membrane Protein GlpF Unfolds via a Dimeric Folding Intermediate. Biochemistry 2011; 50:10223-30. [DOI: 10.1021/bi201266m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anbazhagan Veerappan
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
- Institut für Biochemie
und Molekularbiologie, ZBMZ, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
| | - Florian Cymer
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
- Institut für Biochemie
und Molekularbiologie, ZBMZ, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
| | - Noreen Klein
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
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Interaction between sodium dodecyl sulfate and membrane reconstituted aquaporins: A comparative study of spinach SoPIP2;1 and E. coli AqpZ. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2600-7. [DOI: 10.1016/j.bbamem.2011.05.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 01/13/2023]
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Kim TY, Schlieter T, Haase S, Alexiev U. Activation and molecular recognition of the GPCR rhodopsin--insights from time-resolved fluorescence depolarisation and single molecule experiments. Eur J Cell Biol 2011; 91:300-10. [PMID: 21803442 DOI: 10.1016/j.ejcb.2011.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022] Open
Abstract
The cytoplasmic surface of the G-protein coupled receptor (GPCR) rhodopsin is a key element in membrane receptor activation, molecular recognition by signalling molecules, and receptor deactivation. Understanding of the coupling between conformational changes in the intramembrane domain and the membrane-exposed surface of the photoreceptor rhodopsin is crucial for the elucidation of the molecular mechanism in GPCR activation. As little is known about protein dynamics, particularly the conformational dynamics of the cytoplasmic surface elements on the nanoseconds timescale, we utilised time-resolved fluorescence anisotropy experiments and site-directed fluorescence labelling to provide information on both, conformational space and motion. We summarise our recent advances in understanding rhodopsin dynamics and function using time-resolved fluorescence depolarisation and single molecule fluorescence experiments, with particular focus on the amphipathic helix 8, lying parallel to the cytoplasmic membrane surface and connecting transmembrane helix 7 with the long C-terminal tail.
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Affiliation(s)
- Tai-Yang Kim
- Physics Department, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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