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Sousa B, Domingues I, Nunes B. A fish perspective on SARS-CoV-2: Toxicity of benzalkonium chloride on Danio rerio. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 102:104200. [PMID: 37394081 DOI: 10.1016/j.etap.2023.104200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
SARS-CoV-2 outbreak led to an increased marketing of disinfectants, creating a potential environmental problem. For instance, pre-pandemic environmental levels of the disinfectant benzalkonium chloride (BAC) ranging from 0.5 to 5 mgL-1 in effluents were expected to further increase threatening aquatic life. Our aim was to characterize potential adverse effects after an acute exposure of zebrafish to different concentrations of BAC. An increase in the overall swimming activity, thigmotaxis behavior, and erratic movements were observed. An increase in CYP1A1 and catalase activities, but inhibitions of CY1A2, GSTs and GPx activities were also noticed. BAC is metabolized by CYP1A1, increasing the production of H2O2, thereby activating the antioxidant enzyme CAT. Data also showed an increase of AChE activity. Our study highlights adverse embryonic, behavioral, and metabolic effects of noteworthy environmental significance, especially considering that the use and release of BAC is most likely to increase in a near future.
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Affiliation(s)
- Beatriz Sousa
- Centro de Estudos do Ambiente e do Mar (CESAM), Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Departamento De Biologia, Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Inês Domingues
- Centro de Estudos do Ambiente e do Mar (CESAM), Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Departamento De Biologia, Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Bruno Nunes
- Centro de Estudos do Ambiente e do Mar (CESAM), Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Departamento De Biologia, Universidade De Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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2
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Bang G, Lee H, Kim H, Han EH, Park YH, Kim JY. Comparison of protein characterization using In solution and S-Trap digestion methods for proteomics. Biochem Biophys Res Commun 2021; 589:197-203. [PMID: 34922203 DOI: 10.1016/j.bbrc.2021.12.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/02/2022]
Abstract
Protein extraction and digestion are important analytical steps in the study of proteomics. The use of sodium dodecyl sulfate (SDS) buffer makes it possible to effectively analyze various proteins. Its use was evaluated using the S-Trap digestion method and compared to the traditional In solution digestion method. Differences in protein composition were examined for each protein preparation method. S-Trap digestion followed by SDS buffer extraction clearly increased the number of identified proteins, including more mitochondrial and membrane-related proteins. The S-Trap digestion method with 5% SDS buffer was applied to the pellet remaining from the removal of RIPA buffer-soluble proteins, which identified more extracellular space proteins than the conventional S-Trap digestion method. S-Trap digestion of the pellet was particularly advantageous for identifying proteins located inside multilayer membranes.
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Affiliation(s)
- Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea; Metabolomics Laboratory, College of Pharmacy, Korea University, Sejong, 30019, Republic of Korea
| | - Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Hyejin Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea
| | - Eun Hee Han
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea
| | - Youngja Hwang Park
- Metabolomics Laboratory, College of Pharmacy, Korea University, Sejong, 30019, Republic of Korea.
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea.
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3
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Nigam P. Thermodynamic quantification of sodium dodecyl sulfate penetration in cholesterol and phospholipid monolayers. Chem Phys Lipids 2020; 232:104974. [DOI: 10.1016/j.chemphyslip.2020.104974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 01/13/2023]
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4
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Zhang Y, Yin S, Zhang B, Bi J, Liu Y, Su Z. HBc-based virus-like particle assembly from inclusion bodies using 2-methyl-2, 4-pentanediol. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Efficient renaturation of inclusion body proteins denatured by SDS. Biochem Biophys Res Commun 2017; 490:1250-1253. [DOI: 10.1016/j.bbrc.2017.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/02/2017] [Indexed: 10/19/2022]
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6
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Krüger D, Kamerlin SCL. Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations. ACS OMEGA 2017; 2:4524-4530. [PMID: 28884160 PMCID: PMC5579539 DOI: 10.1021/acsomega.7b00820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/01/2017] [Indexed: 06/07/2023]
Abstract
Micelles play an important role in both experimental and computational studies of the effect of lipid interactions on biological systems. The spherical geometry and the dynamical behavior of micelles makes generating micelle structures for use in molecular simulations challenging. An easy tool for generating simulation-ready micelle models, covering a broad range of lipids, is highly desirable. Here, we present a new Web server, Micelle Maker, which can provide equilibrated micelle models as a direct input for subsequent molecular dynamics simulations from a broad range of lipids (currently 25 lipid types, including 24 glycolipids). The Web server, which is available at http://www.micellemaker.net, uses error checking routines to prevent clashes during the initial placement of the lipids and uses AMBER's GLYCAM library for generating minimized or equilibrated micelle models, but the resulting structures can be used as starting points for simulations with any force field or simulation package. Extensive validation simulations with an overall simulation time of 12 μs using eight micelle models where assembly information is available show that all of the micelles remain very stable over the whole simulation time. Finally, we discuss the advantages of Micelle Maker relative to other approaches in the field.
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Affiliation(s)
- Dennis
M. Krüger
- Science for Life Laboratory,
Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Box 596, S-754 21 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science for Life Laboratory,
Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Box 596, S-754 21 Uppsala, Sweden
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7
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Hepatitis C Virus Envelope Glycoprotein E1 Forms Trimers at the Surface of the Virion. J Virol 2015; 89:10333-46. [PMID: 26246575 DOI: 10.1128/jvi.00991-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/13/2015] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED In hepatitis C virus (HCV)-infected cells, the envelope glycoproteins E1 and E2 assemble as a heterodimer. To investigate potential changes in the oligomerization of virion-associated envelope proteins, we performed SDS-PAGE under reducing conditions but without thermal denaturation. This revealed the presence of SDS-resistant trimers of E1 in the context of cell-cultured HCV (HCVcc) as well as in the context of HCV pseudoparticles (HCVpp). The formation of E1 trimers was found to depend on the coexpression of E2. To further understand the origin of E1 trimer formation, we coexpressed in bacteria the transmembrane (TM) domains of E1 (TME1) and E2 (TME2) fused to reporter proteins and analyzed the fusion proteins by SDS-PAGE and Western blotting. As expected for strongly interacting TM domains, TME1-TME2 heterodimers resistant to SDS were observed. These analyses also revealed homodimers and homotrimers of TME1, indicating that such complexes are stable species. The N-terminal segment of TME1 exhibits a highly conserved GxxxG sequence, a motif that is well documented to be involved in intramembrane protein-protein interactions. Single or double mutations of the glycine residues (Gly354 and Gly358) in this motif markedly decreased or abrogated the formation of TME1 homotrimers in bacteria, as well as homotrimers of E1 in both HCVpp and HCVcc systems. A concomitant loss of infectivity was observed, indicating that the trimeric form of E1 is essential for virus infectivity. Taken together, these results indicate that E1E2 heterodimers form trimers on HCV particles, and they support the hypothesis that E1 could be a fusion protein. IMPORTANCE HCV glycoproteins E1 and E2 play an essential role in virus entry into liver cells as well as in virion morphogenesis. In infected cells, these two proteins form a complex in which E2 interacts with cellular receptors, whereas the function of E1 remains poorly understood. However, recent structural data suggest that E1 could be the protein responsible for the process of fusion between viral and cellular membranes. Here we investigated the oligomeric state of HCV envelope glycoproteins. We demonstrate that E1 forms functional trimers after virion assembly and that in addition to the requirement for E2, a determinant for this oligomerization is present in a conserved GxxxG motif located within the E1 transmembrane domain. Taken together, these results indicate that a rearrangement of E1E2 heterodimer complexes likely occurs during the assembly of HCV particles to yield a trimeric form of the E1E2 heterodimer. Gaining structural information on this trimer will be helpful for the design of an anti-HCV vaccine.
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8
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Yang Z, Wang C, Zhou Q, An J, Hildebrandt E, Aleksandrov LA, Kappes JC, DeLucas LJ, Riordan JR, Urbatsch IL, Hunt JF, Brouillette CG. Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains. Protein Sci 2014; 23:769-89. [PMID: 24652590 PMCID: PMC4093953 DOI: 10.1002/pro.2460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/06/2022]
Abstract
Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Chi Wang
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Jianli An
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
| | - Luba A Aleksandrov
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - John C Kappes
- Department of Medicine, University of Alabama at BirminghamBirmingham, Alabama
- Birmingham Veterans Affairs Medical Center, Research ServiceBirmingham, Alabama
| | - Lawrence J DeLucas
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
- Department of Optometry, University of Alabama at BirminghamBirmingham, Alabama
| | - John R Riordan
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
- Center for Membrane Protein Research, Texas Tech University Health Sciences CenterLubbock, TX
| | - John F Hunt
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Christie G Brouillette
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
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9
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Abstract
Commonly used detergent sclerosants including sodium tetradecyl sulphate (STS) and polidocanol (POL) are clinically used to induce endovascular fibrosis and vessel occlusion. They achieve this by lysing the endothelial lining of target vessels. These agents are surface active (surfactant) molecules that interfere with cell membranes. Surfactants have a striking similarity to the phospholipid molecules of the membrane lipid bilayer. By adsorbing at the cell membrane, surfactants disrupt the normal architecture of the lipid bilayer and reduce the surface tension. The outcome of this interaction is concentration dependent. At high enough concentrations, surfactants solubilise cell membranes resulting in cell lysis. At lower concentrations, these agents can induce a procoagulant negatively charged surface on the external aspect of the cell membrane. The interaction is also influenced by the ionic charge, molecular structure, pH and the chemical nature of the diluent (e.g. saline vs. water). The ionic charge of the surfactant molecule can influence the effect on plasma proteins and the protein contents of cell membranes. STS, an anionic detergent, denatures the tertiary complex of most proteins and in particular the clinically relevant clotting factors. By contrast, POL has no effect on proteins due to its non-ionic structure. These agents therefore exhibit remarkable differences in their interaction with lipid membranes, target cells and circulating proteins with potential implications in a range of clinical applications.
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Affiliation(s)
- Kurosh Parsi
- Dermatology, Phlebology and Fluid Mechanics Research Laboratory, St Vincent's Centre for Applied Medical Research, The University of New South Wales, Sydney, Australia
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10
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Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Expert Rev Proteomics 2012; 8:787-800. [PMID: 22087661 DOI: 10.1586/epr.11.67] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Proteome fractionation refers to separation at the level of intact proteins. Proteome fractionation may precede sample digestion and subsequent peptide-level separation and detection (i.e., bottom-up mass spectrometry [MS]). For top-down MS, proteome fractionation acts as a stand-alone separation platform, since intact proteins are directly analyzed by the mass spectrometer. Regardless of the MS identification strategy, separation of intact proteins has clear benefits as a result of decreasing sample complexity. However, this stage of the workflow also creates considerable challenges, which are generally absent from the counterpart peptide separation experiment. For example, maintaining protein solubility is a key concern before, during and after separation. To this end, surfactants such as sodium dodecyl sulfate may be employed during fractionation, so long as they are eliminated prior to MS. In this article, current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada.
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11
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Zhou J, Hu Y, Lin Y, Liu H, Xie P. Preparation and application of a partially degradable gel in mass spectrometry-based proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2957-62. [DOI: 10.1016/j.jchromb.2011.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/13/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
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12
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Zhou J, Li J, Li J, Chen P, Wang X, Liang S. Dried polyacrylamide gel absorption: a method for efficient elimination of the interferences from SDS-solubilized protein samples in mass spectrometry-based proteome analysis. Electrophoresis 2011; 31:3816-22. [PMID: 21064138 DOI: 10.1002/elps.201000255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sample preparation holds an important place in MS-based proteome analysis. For effective proteolysis and MS analysis, it is essential to eliminate the interferences while extracting the analytes of interest from complex mixtures. To address this, herein we describe a new dried polyacrylamide gel absorption method. In this method, the protein sample prepared using high concentration of SDS was directly and completely absorbed by vacuum-dried polyacrylamide gel, and then the interfering substances including SDS and some other salts were efficiently removed by in-gel washing steps while retaining the denatured proteins in the gel, thus offering a clean environment amenable to downstream buffer exchange, proteolytic digestion and digest recovery, etc. In combination with in-gel digestion and LC-MS/MS, the newly developed method was applied to the proteome analyses of membrane-enriched fraction and whole tissue homogenate. It was demonstrated that the method is suitable for the analysis of a complex biological sample and can be widely used for sample cleanup in shotgun proteome analyses.
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Affiliation(s)
- Jian Zhou
- The Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, PR China
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13
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Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
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14
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Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T, Drabik A, Suder P, Noga M, Jarzebinska J, Silberring J. Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:1-31. [PMID: 17113834 DOI: 10.1016/j.jchromb.2006.10.040] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 10/23/2006] [Indexed: 01/04/2023]
Abstract
Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.
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Affiliation(s)
- Anna Bodzon-Kulakowska
- Department of Neurobiochemistry, Faculty of Chemistry, Jagiellonian University, Ingardena St. 3, 30-060 Krakow, Poland
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15
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Hartmann SU, Wigdahl B, Neely EB, Berlin CM, Schengrund CL, Lin HM, Howett MK. Biochemical analysis of human milk treated with sodium dodecyl sulfate, an alkyl sulfate microbicide that inactivates human immunodeficiency virus type 1. J Hum Lact 2006; 22:61-74. [PMID: 16467288 DOI: 10.1177/0890334405280651] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Reduction of transmission of human immunodeficiency virus type 1 (HIV-1) through human milk is needed. Alkyl sulfates such as sodium dodecyl sulfate (SDS) are microbicidal against HIV-1 at low concentrations, have little to no toxicity, and are inexpensive. The authors have reported that treatment of HIV-1-infected human milk with < or = 1% (10 mg/mL) SDS for 10 minutes inactivates cell-free and cell-associated virus. The SDS can be removed with a commercially available resin after treatment without recovery of viral infectivity. In this article, the authors report results of selective biochemical analyses (ie, protein, immunoglobulins, lipids, cells, and electrolytes) of human milk subjected to SDS treatment and removal. The SDS treatment or removal had no significant effects on the milk components studied. Therefore, the use of alkyl sulfate microbicides to treat milk from HIV-1-positive women may be a simple, practical, and nutritionally sound way to prevent or reduce transmission of HIV-1 while still feeding with mother's own milk.
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Affiliation(s)
- Sandra Urdaneta Hartmann
- Department of Microbiology and Immunology, Pennsylvania State University, College of Medicine, Hershey, USA
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16
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Barakat S, Gayet L, Dayan G, Labialle S, Lazar A, Oleinikov V, Coleman A, Baggetto L. Multidrug-resistant cancer cells contain two populations of P-glycoprotein with differently stimulated P-gp ATPase activities: evidence from atomic force microscopy and biochemical analysis. Biochem J 2005; 388:563-71. [PMID: 15693753 PMCID: PMC1138964 DOI: 10.1042/bj20041999] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Considerable interest exists about the localization of P-gp (P-glycoprotein) in DRMs (detergent-resistant membranes) of multidrug resistant cancer cells, in particular concerning the potential modulating role of the closely related lipids and proteins on P-gp activity. Our observation of the opposite effect of verapamil on P-gp ATPase activity from DRM and solubilized-membrane fractions of CEM-resistant leukaemia cells, and results from Langmuir experiments on membrane monolayers from resistant CEM cells, strongly suggest that two functional populations of P-gp exist. The first is located in DRM regions: it displays its optimal P-gp ATPase activity, which is almost completely inhibited by orthovanadate and activated by verapamil. The second is located elsewhere in the membrane; it displays a lower P-gp ATPase activity that is less sensitive to orthovanadate and is inhibited by verapamil. A 40% cholesterol depletion of DRM caused the loss of 52% of the P-gp ATPase activity. Cholesterol repletion allowed recovery of the initial P-gp ATPase activity. In contrast, in the solubilized-membrane-containing fractions, cholesterol depletion and repletion had no effect on the P-gp ATPase activity whereas up to 100% saturation with cholesterol induced a 58% increased P-gp ATPase activity, while no significant modification was observed for the DRM-enriched fraction. DRMs were analysed by atomic force microscopy: 40-60% cholesterol depletion was necessary to remove P-gp from DRMs. In conclusion, P-gp in DRMs appears to contain closely surrounding cholesterol that can stimulate P-gp ATPase activity to its optimal value, whereas cholesterol in the second population seems deprived of this function.
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Affiliation(s)
- Stéphane Barakat
- *Thérapie transcriptionnelle des cellules cancéreuses, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Landry Gayet
- *Thérapie transcriptionnelle des cellules cancéreuses, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Guila Dayan
- *Thérapie transcriptionnelle des cellules cancéreuses, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Stéphane Labialle
- †McGill University, Royal Victoria Hospital, F3.32, 687 Pine avenue West, Montreal, QC, Canada H3A 1A1
| | - Adina Lazar
- ‡Assemblages moléculaires d'intérêt biologique, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Vladimir Oleinikov
- §Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow B-437, GSP 117997, Russia
| | - Anthony W. Coleman
- ‡Assemblages moléculaires d'intérêt biologique, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Loris G. Baggetto
- *Thérapie transcriptionnelle des cellules cancéreuses, IBCP - UMR 5086 CNRS UCBL, 7 Passage du Vercors, 69367 Lyon cedex 07, France
- To whom correspondence should be addressed (email )
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17
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Seddon AM, Curnow P, Booth PJ. Membrane proteins, lipids and detergents: not just a soap opera. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1666:105-17. [PMID: 15519311 DOI: 10.1016/j.bbamem.2004.04.011] [Citation(s) in RCA: 904] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Studying membrane proteins represents a major challenge in protein biochemistry, with one of the major difficulties being the problems encountered when working outside the natural lipid environment. In vitro studies such as crystallization are reliant on the successful solubilization or reconstitution of membrane proteins, which generally involves the careful selection of solubilizing detergents and mixed lipid/detergent systems. This review will concentrate on the methods currently available for efficient reconstitution and solubilization of membrane proteins through the use of detergent micelles, mixed lipid/detergent micelles and bicelles or liposomes. We focus on the relevant molecular properties of the detergents and lipids that aid understanding of these processes. A significant barrier to membrane protein research is retaining the stability and function of the protein during solubilization, reconstitution and crystallization. We highlight some of the lessons learnt from studies of membrane protein folding in vitro and give an overview of the role that lipids can play in stabilizing the proteins.
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Affiliation(s)
- Annela M Seddon
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
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Sedzik J, Uyemura K, Tsukihara T. Towards crystallization of hydrophobic myelin glycoproteins: P0 and PASII/PMP22. Protein Expr Purif 2002; 26:368-77. [PMID: 12460760 DOI: 10.1016/s1046-5928(02)00564-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The preparation of a pure and homogeneous protein sample at proper concentration is a prerequisite for success when attempting their crystallization for structural determination. The detergents suitable for solubilization particularly of membrane proteins are not always the best for crystallization. Myelin of the peripheral nervous system of vertebrates is the example of a membrane for which neutral or "gentle" detergents are not even strong enough to solubilize its proteins. In contrast, sodium- or lithium-dodecyl sulfate is very effective. We solubilized myelin membrane in 2%(w/v) sodium dodecyl sulfate, followed by chromatographic purification of the hydrophobic myelin glycoproteins P0 and PASII/PMP22, and finally, we have exchanged the sodium dodecyl sulfate bound to protein for other neutral detergents using ceramic hydroxyapatite column. Theoretically, we should easily exchange sodium dodecyl sulfate for any neutral detergent, but for some of them, the solubility of myelin glycoproteins is low. To monitor the potential variability in the secondary structure of glycoproteins, we have used circular dichroism. Sodium dodecyl sulfate seems to be the appropriate detergent for the purpose of purification of very hydrophobic glycoproteins, since it can be easily exchanged for another neutral detergent.
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Affiliation(s)
- Jan Sedzik
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
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19
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Meng FG, Zeng X, Hong YK, Zhou HM. Dissociation and unfolding of GCN4 leucine zipper in the presence of sodium dodecyl sulfate. Biochimie 2001; 83:953-6. [PMID: 11728632 DOI: 10.1016/s0300-9084(01)01340-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The dissociation and unfolding behavior of the GCN4 leucine zipper has been studied using SDS titration. Circular dichroism (CD) spectra showed that the alpha-helix content of the leucine zipper (20 microM) decreased during the sodium dodecyl sulfate (SDS) titration. However, the alpha-helix content of the leucine zipper still remained significant in the presence of 1 mM SDS, with little change detected when the SDS concentration further increased to 2 mM. The dimer dissociation of the leucine zipper is also a co-operative process during SDS titration; with no dimer remaining when SDS concentration reached 1 mM, as shown by electrophoresis and the the theta(222)/theta(208) ratio. Our results indicate that SDS efficiently induces leucine zipper dimer dissociation with the monomers still partially folded. The experimental results provide important evidence for the previous model that partial helix formation precedes dimerization in coiled coil folding.
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Affiliation(s)
- F G Meng
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
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20
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Rusconi F, Valton E, Nguyen R, Dufourc E. Quantification of sodium dodecyl sulfate in microliter-volume biochemical samples by visible light spectroscopy. Anal Biochem 2001; 295:31-7. [PMID: 11476542 DOI: 10.1006/abio.2001.5164] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A method for sodium dodecyl sulfate (SDS) quantitation in microliter-volume complex biochemical samples is described. The quantitation is based on the use of a dye, stains-all, the color of which changes from intense fuchsia to yellow upon addition of SDS. We show that this color change is gradual and proportional to the amount of SDS added to the stains-all solution, thus allowing its use to reliably quantitate SDS in biochemical samples by means of a visible light spectrophotometer. A large number of compounds widely used in biochemistry are herein shown not to interfere with the SDS measurement when they are present in the sample at usual biochemical concentrations. Furthermore, linearity between the color change and the amount of SDS present in the sample is never impaired when huge amounts of these compounds are also present, thus making this quantitation method highly reliable with use of a calibration curve. The method allows easy and reliable quantitation of microgram amounts of SDS in microliter-volume biochemical samples.
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Affiliation(s)
- F Rusconi
- Institut Européen de Chimie et Biologie, ENSCPB, Avenue Pey Berland, Talence Cedex, F-33402,
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21
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le Maire M, Champeil P, Moller JV. Interaction of membrane proteins and lipids with solubilizing detergents. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:86-111. [PMID: 11090820 DOI: 10.1016/s0304-4157(00)00010-1] [Citation(s) in RCA: 722] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Detergents are indispensable in the isolation of integral membrane proteins from biological membranes to study their intrinsic structural and functional properties. Solubilization involves a number of intermediary states that can be studied by a variety of physicochemical and kinetic methods; it usually starts by destabilization of the lipid component of the membranes, a process that is accompanied by a transition of detergent binding by the membrane from a noncooperative to a cooperative interaction already below the critical micellar concentration (CMC). This leads to the formation of membrane fragments of proteins and lipids with detergent-shielded edges. In the final stage of solubilization membrane proteins are present as protomers, with the membrane inserted sectors covered by detergent. We consider in detail the nature of this interaction and conclude that in general binding as a monolayer ring, rather than as a micelle, is the most probable mechanism. This mode of interaction is supported by neutron diffraction investigations on the disposition of detergent in 3-D crystals of membrane proteins. Finally, we briefly discuss the use of techniques such as analytical ultracentrifugation, size exclusion chromatography, and mass spectrometry relevant for the structural investigation of detergent solubilized membrane proteins.
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Affiliation(s)
- M le Maire
- Unite de recherche Associée 2096 (Centre National de la Recherche Scientifique et Commissariat a l'Energie Atomique), Cedex, France.
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22
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Hydroxyapatite Chromatography. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0301-4770(08)60533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Sedzik J, Kotake Y, Uyemura K. Purification of P0 myelin glycoprotein by a Cu2+-immobilized metal affinity chromatography. Neurochem Res 1999; 24:723-32. [PMID: 10447455 DOI: 10.1023/a:1020723328143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
P0 is an abundant myelin glycoprotein of peripheral nerves of vertebrates. Various point mutations of this protein are responsible for hereditary neuropathies. In this paper we described purification of P0 glycoprotein using SDS and a metal chelate affinity chromatography. Purified myelin fraction from bovine spinal roots in 0.5% SDS, 0.5 M NaCl, 50 mM Tris-HCl, pH 7.4 is filtered and applied directly to the Cu2+-immobilized affinity chromatography column, equilibrated with the same buffer. After eluting a void volume (or pass through) fraction, P0 protein was eluted by the same buffer but without salt. To remove contamination from the eluent, further purification is continued on a Concanavalin-A coupled agarose column. We purify within two days, 30 mg of P0 protein of apparent molecular weight 27 kDa. The method can be used to purify recombinant or mutated P0 protein found in severe pathologies.
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Affiliation(s)
- J Sedzik
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
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Li F, Dong M, Miller LJ, Naylor S. Efficient removal of sodium dodecyl sulfate (SDS) enhances analysis of proteins by SDS-polyacrylamide gel electrophoresis coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:464-465. [PMID: 10209878 DOI: 10.1002/(sici)1097-0231(19990315)13:5<464::aid-rcm486>3.0.co;2-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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26
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Yvon S, Rolland D, Charrier JP, Jolivet M. An alternative for purification of low soluble recombinant hepatitis C virus core protein: preparative two-dimensional electrophoresis. Electrophoresis 1998; 19:1300-5. [PMID: 9694269 DOI: 10.1002/elps.1150190814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
For isolation of low soluble recombinant full-length (amino acids 1-191) core protein of hepatitis C virus (HCV) overexpressed in Escherichia coli, the advantage of combining two electrophoretic techniques, in comparison with chromatographic separation, is demonstrated. The protein extract was first solubilized in agents compatible with electrophoretic separation. Using preparative liquid phase isoelectric focusing (IEF) the protein of interest was first concentrated within a defined acidic pH range. These fractions were then submitted to preparative sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE) to isolate the 22 kDa protein. The second-dimensional step allowed the isolation of 2 mg of the purified recombinant HCV core protein (rHCV-C191) from 1.5 g bacterial pellet. This quantity is sufficient to characterize the protein and to perform immunogenicity studies. This procedure of two-dimensional preparative electrophoresis is applicable to a wide range of biological samples and represents an alternative for purification of insoluble proteins.
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Affiliation(s)
- S Yvon
- Département Recherche et Développement, Unité Immunoassays, BioMérieux S.A., Marcy-l'Etoile, France
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27
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Dong M, Ladavière L, Penin F, Deléage G, Baggetto LG. Secondary structure of P-glycoprotein investigated by circular dichroism and amino acid sequence analysis. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1371:317-34. [PMID: 9630701 DOI: 10.1016/s0005-2736(98)00032-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
P-glycoprotein (Pgp) is a plasma membrane protein known as an ATP-dependent drug-efflux pump that confers multidrug resistance to tumor cells. Structural analysis of Pgp was investigated by circular dichroism (CD) for the first time and in combination with amino acid sequence analysis. CD of highly purified Pgp from human, rat and murine Pgp-overexpressing drug resistant cells revealed slight variations in the spectral shape when recorded in the presence of dodecyl maltoside (DM). These species-dependent variations in CD shapes resulted from the interaction of the oligosaccharidic part with the protein core since they were abolished either in the presence of sodium dodecyl sulfate (SDS) or after deglycosylation, the latter not altering the Pgp ATP-dependent drug transport activity. Whatever the level of Pgp glycosylation and the detergent used (SDS or DM), the content in secondary structure deduced from deconvolution of CD spectra is almost the same for the three sources of Pgp and estimated to 43% alpha-helix, 16% beta-sheet, 15% beta-turn and 26% of other structures. These data, which constitute the first report of Pgp structure analysis by circular dichroism, are consistent with the 48% alpha-helix and 16% beta-sheets global contents predicted by using recently reported efficient secondary structure prediction methods. This consistency reinforces the reliability of the probable nature and localization of predicted Pgp secondary structure elements. This provides a good framework for precise 3D structure modeling of Pgp by homology with proteins of known 3D structure, as it is illustrated here for the A motifs of the ATP-binding domains of Pgp.
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Affiliation(s)
- M Dong
- Institut de Biologie et Chimie des Protéines, UPR 412 CNRS, 7 Passage du Vercors F-69367, Lyon Cedex 07, France
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28
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Pomroy NC, Deber CM. Solubilization of hydrophobic peptides by reversible cysteine PEGylation. Biochem Biophys Res Commun 1998; 245:618-21. [PMID: 9571204 DOI: 10.1006/bbrc.1998.8493] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
"PEG-a-Cys" reagent, synthesized by the esterification of monomethoxy-poly(ethylene glycol) (avg. MW = 5 kDa) to Ellman's reagent [5,5'-dithiobis(2-nitrobenzoic acid)], is shown to "PEGylate" reversibly the cysteine residue of a 25-residue synthetic hydrophobic peptide (H2N-REAAALAAAAALAAWAALCPARRRR-CO2H) designed to model a transmembrane segment of a membrane protein. A mixed disulfide bond was formed between the reagent and the peptide that was readily cleaved with the mild reducing agent tricarboxyethylphosphine hydrochloride (TCEP.HCl). Carboxypeptidase B digestion of the charged carboxyl terminus of the peptide through to the Ala residue--which mimics the enzymatic cleavage of a TM segment from a fusion protein--releases a highly hydrophobic peptide. A time-dependent decrease in the amplitude of the digested peptide circular dichroism (CD) spectra was attributed to the aggregation and/or precipitation of the peptide. While PEGylation of the peptide with PEG-a-Cys had a negligible effect on conformation, it inhibited the loss of CD amplitude in both intact and digested peptides, suggesting that it was effective in solubilization of hydrophobic peptides.
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Affiliation(s)
- N C Pomroy
- Division of Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada
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