1
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Cross-linking of bovine rhodopsin with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate affects its functionality. Biochem J 2020; 477:2295-2312. [PMID: 32497171 DOI: 10.1042/bcj20200376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 02/08/2023]
Abstract
Rhodopsin is the photoreceptor protein involved in visual excitation in retinal rods. The functionality of bovine rhodopsin was determined following treatment with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC), a bifunctional reagent capable of forming covalent cross-links between suitable placed lysines and cysteines. Denaturing polyacrylamide gel electrophoresis showed that rhodopsin incubated with sulfo-SMCC generated intermolecular dimers, trimers, and higher oligomers, although most of the sulfo-SMCC-treated protein remained as a monomer. Minor alterations on the absorption spectrum of light-activated sulfo-SMCC-treated rhodopsin were observed. However, only ∼2% stimulation of the guanine nucleotide binding activity of transducin was measured in the presence of sulfo-SMCC-cross-linked photolyzed rhodopsin. Moreover, rhodopsin kinase was not able of phosphorylating sulfo-SMCC-cross-linked rhodopsin after illumination. Rhodopsin was purified in the presence of either 0.1% or 1% n-dodecyl β-d-maltoside, to obtain dimeric and monomeric forms of the protein, respectively. Interestingly, no generation of the regular F1 and F2 thermolytic fragments was perceived with sulfo-SMCC-cross-linked rhodopsin either in the dimeric or monomeric state, implying the formation of intramolecular connections in the protein that might thwart the light-induced conformational changes required for interaction with transducin and rhodopsin kinase. Structural analysis of the rhodopsin three-dimensional structure suggested that the following lysine and cysteine pairs: Lys66/Lys67 and Cys316, Cys140 and Lys141, Cys140 and Lys248, Lys311 and Cys316, and/or Cys316 and Lys325 are potential candidates to generate intramolecular cross-links in the protein. Yet, the lack of fragmentation of sulfo-SMCC-treated Rho with thermolysin is consistent with the formation of cross-linking bridges between Lys66/Lys67 and Cys316, and/or Cys140 and Lys248.
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2
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Rodríguez S, Silva ML, Benaím G, Bubis J. Phosphorylation-induced conformational changes of photoactivated rhodopsin probed by fluorescent labeling at Cys 140 and Cys 316. Biochimie 2018; 150:57-69. [PMID: 29730301 DOI: 10.1016/j.biochi.2018.04.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/29/2018] [Indexed: 11/28/2022]
Abstract
In order to monitor conformational changes following photoactivation and phosphorylation of bovine rhodopsin, the two reactive sulfhydryl groups at Cys140 and Cys316 were specifically labeled with the monobromobimane (mBBr) fluorophore. Although alterations in conformation after light exposure of rhodopsin were not detected by fluorescence excitation scans (300-450 nm) of the mBBr-labeled protein, the fluorescence signal was reduced ∼ 90% in samples containing photoactivated phosphorhodopsin. Predominant labeling at either Cys140 or Cys316 in light-activated and phosphorylated rhodopsin merely generated a decrease of ∼38% and 28%, respectively, in the fluorescence excitation intensity. Thus, neither mBBr-modified Cys140 nor mBBr-modified Cys316 were involved single-handedly in the remarkable fall seen on the signal following phosphorylation of the protein; rather, the incorporation of phosphate groups on the mBBr-labeled light-activated rhodopsin appeared to affect its fluorescence signal in a cooperative or synergistic manner. These findings demonstrated that the phosphorylation of specific hydroxyl groups at the carboxyl terminal tail of rhodopsin causes definite conformational changes in the three-dimensional fold of the protein. Apparently, amino acid residues that are buried in the interior of the inactive protein become accessible following illumination and phosphorylation of rhodopsin, quenching in turn the fluorescence excitation signal of mBBr-modified rhodopsin.
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Affiliation(s)
- Sheerly Rodríguez
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas, Venezuela; Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela.
| | - May-Li Silva
- Instituto de Estudios Avanzados IDEA, Caracas, Venezuela.
| | - Gustavo Benaím
- Instituto de Estudios Avanzados IDEA, Caracas, Venezuela; Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela.
| | - José Bubis
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas, Venezuela.
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3
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Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
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Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
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4
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Wu YL, Li J, Yao K. Structures and biogenetic analysis of lipofuscin bis-retinoids. J Zhejiang Univ Sci B 2014; 14:763-73. [PMID: 24009196 DOI: 10.1631/jzus.b1300051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Age-related macular degeneration (AMD) is still an incurable blinding eye disease because of complex pathogenic mechanisms and unusual diseased regions. With the use of chemical biology tools, great progress has been achieved in improving the understanding of AMD pathogenesis. The severity of AMD is, at least in part, linked to the non-degradable lipofuscin bis-retinoids in retinal pigment epithelial (RPE). This material is thought to result from the lifelong accumulation of lysosomal residual bodies containing the end products derived from the daily phagocytosis of rod outer segments by RPE cells. Here, we present previously recognized bis-retinoids with focus on structures and biosynthetic pathways. In addition to a brief discussion on the mutual conversion relationships of bis-retinoids, future perspectives and the medical relevance of such studies on these lipofuscin constituents are also highlighted.
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Affiliation(s)
- Ya-lin Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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5
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Furuta T, Mochizuki M, Ito M, Takahashi T, Suzuki T, Kan T. Versatile synthesis of head group functionalized phospholipids via oxime bond formation. Org Lett 2008; 10:4847-50. [PMID: 18823121 DOI: 10.1021/ol8019346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A method for introduction of various head groups on phospholipid frameworks via oxime bond formation has been developed for the synthesis of cyclen-Cu(II), pyrene, naphthalene, and other headgroup functionalized phospholipids that can cleave the membrane protein, hemagglutinin.
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Affiliation(s)
- Takumi Furuta
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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6
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Chen SH, Liao HK, Chang CY, Juo CG, Chen JH, Chan SI, Chen YJ. Targeted protein quantitation and profiling using PVDF affinity probe and MALDI-TOF MS. Proteomics 2007; 7:3038-50. [PMID: 17676666 DOI: 10.1002/pmic.200700393] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Development of a rapid, effective, and highly specific platform for target identification in complex biofluids is one of the most important tasks in proteomic research. Taking advantage of the natural hydrophobic interaction of PVDF with probe protein, a simple and effective method was developed for protein quantitation and profiling. Using antibody-antigen interactions as a proof-of-concept system, the targeted plasma proteins, serum amyloid P (SAP), serum amyloid A (SAA), and C-reactive protein (CRP), could be selectively isolated and enriched from human plasma by antibody-immobilized PVDF membrane and directly identified by MALDI-TOF MS without additional elution step. The approach was successfully applied to human plasma for rapid quantitation and variant screening of SAP, SAA, and CRP in healthy individuals and patients with gastric cancer. The triplexed on-probe quantitative analysis revealed significant overexpression of CRP and SAA in gastric cancer group, consistent with parallel ELISA measurements and pathological progression and prognostic significance reported in previous literatures. Furthermore, the variant mass profiling of the post-translationally modified forms revealed a high occurrence of de-sialic acid SAP in patients with gastric cancer. Due to the versatile assay design, ease of probe preparation without chemical synthesis, and compatibility with MALDI-TOF MS analysis, the methodology may be useful for target protein characterization, functional proteomics, and screening in clinical proteomics.
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Affiliation(s)
- Shu-Hua Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, ROC
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7
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Xu G, Chance MR. Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics. Chem Rev 2007; 107:3514-43. [PMID: 17683160 DOI: 10.1021/cr0682047] [Citation(s) in RCA: 513] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guozhong Xu
- Center for Proteomics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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8
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Pluder F, Mörl K, Beck-Sickinger AG. Proteome analysis to study signal transduction of G protein-coupled receptors. Pharmacol Ther 2006; 112:1-11. [PMID: 16644018 DOI: 10.1016/j.pharmthera.2006.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 03/01/2006] [Indexed: 12/28/2022]
Abstract
G protein-coupled receptors (GPCR) play an important role in drug development. Although many classical signal transduction pathways have been elucidated, more and more cross-talk to other cascades, e.g. MAP-kinase have been reported. In order to identify the overall function of receptor stimulation in a specific cell type or under certain conditions proteome analysis has been shown to be a very successful and powerful approach. Here, we will summarize the current state of the art of proteome analysis applied to GPCR.
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Affiliation(s)
- Franka Pluder
- Institute of Biochemistry, University of Leipzig, Brüderstrasse 34, D-04103, Leipzig, Germany
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9
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Mansoor SE, Palczewski K, Farrens DL. Rhodopsin self-associates in asolectin liposomes. Proc Natl Acad Sci U S A 2006; 103:3060-5. [PMID: 16492772 PMCID: PMC1413906 DOI: 10.1073/pnas.0511010103] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Indexed: 11/18/2022] Open
Abstract
We show that the photoreceptor rhodopsin (Rh) can exist in the membrane as a dimer or multimer using luminescence resonance energy transfer and FRET methods. Our approach looked for interactions between Rh molecules reconstituted into asolectin liposomes. The low receptor density used in the measurements ensured minimal receptor crowding and artifactual association. The fluorescently labeled Rh molecules were fully functional, as measured by their ability to activate the G protein transducin. The luminescence resonance energy transfer measurements revealed a distance of 47-50 Angstroms between Rh molecules. The measured efficiency of FRET between receptors was close to the theoretical maximum possible, indicating nearly quantitative Rh-Rh association. Together, these results provide compelling evidence that Rh spontaneously self-associates in membranes.
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Affiliation(s)
- Steven E. Mansoor
- *Department of Biochemistry and Molecular Biology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239-3098; and
| | - Krzysztof Palczewski
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106
| | - David L. Farrens
- *Department of Biochemistry and Molecular Biology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239-3098; and
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10
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Chang CY, Liao HK, Juo CG, Chen SH, Chen YJ. Improved analysis of membrane protein by PVDF-aided, matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2006; 556:237-46. [PMID: 17723354 DOI: 10.1016/j.aca.2005.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 07/13/2005] [Accepted: 07/14/2005] [Indexed: 11/30/2022]
Abstract
Characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. This study presents the utility of the polyvinylidene difluoride (PVDF) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The hydrophobic adsorption of protein, particularly membrane proteins, on the PVDF surface enables efficient on-PVDF washing to remove high concentrations of detergents and salts, such as up to 5% sodium dodecyl sulfate (SDS). The enhanced spectrum quality for MALDI detection is particularly notable for high molecular weight proteins. By using on-PVDF washing prior to MALDI detection, we obtained protein profiles of the detergent-containing and detergent-insoluble membrane fractions from Methylococcus capsulatus (Bath). Similar improvements of signal-to-noise ratios were shown on the MALDI spectra for proteins electroblotted from SDS-polyacrylamide gel electrophoresis (SDS-PAGE) onto the PVDF membrane. We have applied this strategy to obtain intact molecular weights of the particulate methane monooxygenase (pMMO) composed of three intrinsic membrane-bound proteins, PmoA, PmoB, and PmoC. Together with peptide sequencing by tandem mass spectrometry, post-translational modifications including N-terminal acetylation of PmoA and PmoC and alternative C-terminal truncation of PmoB were identified. The above results show that PVDF-aided MALDI-MS can be an effective approach for profiling and characterization of membrane proteins.
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Affiliation(s)
- Chih-Yang Chang
- Institute of Chemistry, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan, ROC
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11
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Furuta T, Sakai M, Hayashi H, Asakawa T, Kataoka F, Fujii S, Suzuki T, Suzuki Y, Tanaka K, Fishkin N, Nakanishi K. Design and synthesis of artificial phospholipid for selective cleavage of integral membrane protein. Chem Commun (Camb) 2005:4575-7. [PMID: 16158119 DOI: 10.1039/b507917a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An artificial phospholipid, possessing saturated alkyl chains as a membrane anchor and protein recognition site as well as an Fe(III)-EDTA moiety as a protein cleavable polar head group, was designed and synthesized based on the amidite method for the purpose of examination of cleavage of integral membrane proteins.
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Affiliation(s)
- Takumi Furuta
- Department of Synthetic Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Shizuoka 422-8526, Japan.
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12
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Suda K, Filipek S, Palczewski K, Engel A, Fotiadis D. The supramolecular structure of the GPCR rhodopsin in solution and native disc membranes. Mol Membr Biol 2005; 21:435-46. [PMID: 15764373 PMCID: PMC1351286 DOI: 10.1080/09687860400020291] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Rhodopsin, the prototypical G-protein-coupled receptor, which is densely packed in the disc membranes of rod outer segments, was proposed to function as a monomer. However, a growing body of evidence indicates dimerization and oligomerization of numerous G-protein-coupled receptors, and atomic force microscopy images revealed rows of rhodopsin dimers in murine disc membranes. In this work we demonstrate by electron microscopy of negatively stained samples, blue native- and sodium dodecyl sulphate-polyacrylamide gel electrophoresis, chemical crosslinking, and by proteolysis that native bovine rhodopsin exists mainly as dimers and higher oligomers. These results corroborate the recent findings from atomic force microscopy and molecular modeling on the supramolecular structure and packing arrangement of murine rhodopsin dimers.
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Affiliation(s)
- Kitaru Suda
- M.E. Müller Institute for Microscopy, Biozentrum, University of Basel, CH-4056Basel, Switzerland
| | - Slawomir Filipek
- International Institute of Molecular and Cell Biology, Warsaw University, Warsaw, PL-02109, Poland
| | - Krzysztof Palczewski
- Departments of Ophthalmology
- Pharmacology, and
- Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Andreas Engel
- M.E. Müller Institute for Microscopy, Biozentrum, University of Basel, CH-4056Basel, Switzerland
| | - Dimitrios Fotiadis
- M.E. Müller Institute for Microscopy, Biozentrum, University of Basel, CH-4056Basel, Switzerland
- *To whom correspondence should be addressed. e-mail:
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13
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Xie XQ, Zhao J, Zheng H. Expression, purification, and isotope labeling of cannabinoid CB2 receptor fragment, CB2180–233. Protein Expr Purif 2004; 38:61-8. [PMID: 15477083 DOI: 10.1016/j.pep.2004.07.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 07/29/2004] [Indexed: 11/18/2022]
Abstract
To develop an approach to obtain milligram quantities of purified isotope-labeled seven transmembrane G-protein coupled cannabinoid (CB) receptor for NMR structural analysis, we chose a truncated CB receptor fragment, CB2(180-233), spanning from the fifth transmembrane domain (TM5) to the associated loop regions of cannabinoid CB2 receptor. This highly hydrophobic membrane protein fragment was pursued for developmental studies of membrane proteins through expression and purification in Escherichia coli. The target peptide was cloned and over-expressed in a preparative scale as a fusion protein with a modified TrpDeltaLE1413 (TrpLE) leader sequence and a nine-histidine tag at its N-terminal. An experimental protocol for enzyme cleavage was developed by using Factor Xa to remove the TrpLE tag from the fusion protein. A purification process was also established using a nickel affinity column and reverse-phase HPLC, and then monitored by SDS-PAGE and MS. This expression level is one of the highest reported for a G-protein coupled receptor and fragments in E. Coli, and provided a sufficient amount of purified protein for further biophysical studies.
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Affiliation(s)
- Xiang-Qun Xie
- Department of Pharmaceutical and Pharmacological Sciences, College of Pharmacy, University of Houston, TX 77247-5037, USA.
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14
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Sale K, Faulon JL, Gray GA, Schoeniger JS, Young MM. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Sci 2004; 13:2613-27. [PMID: 15340162 PMCID: PMC2286557 DOI: 10.1110/ps.04781504] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 06/23/2004] [Accepted: 06/23/2004] [Indexed: 10/26/2022]
Abstract
We present a two-step approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only sparse distance constraints, such as those derived from chemical cross-linking, dipolar EPR and FRET experiments. In Step 1, using an algorithm, we developed, the conformational space of membrane protein folds matching a set of distance constraints is explored to provide initial structures for local conformational searches. In Step 2, these structures refined against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. We begin by describing the statistical analysis of the solved membrane protein structures from which the theoretical portion of the penalty function was derived. We then describe the penalty function, and, using a set of six test cases, demonstrate that it is capable of distinguishing helical bundles that are close to the native bundle from those that are far from the native bundle. Finally, using a set of only 27 distance constraints extracted from the literature, we show that our method successfully recovers the structure of dark-adapted rhodopsin to within 3.2 A of the crystal structure.
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Affiliation(s)
- Ken Sale
- Biosystems Research Department, Sandia National Laboratories, P.O. Box 969, MS 9951, Livermore CA 94551-0969, USA.
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15
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Faulon JL, Sale K, Young M. Exploring the conformational space of membrane protein folds matching distance constraints. Protein Sci 2003; 12:1750-61. [PMID: 12876324 PMCID: PMC2323961 DOI: 10.1110/ps.0305003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Herein we present a computational technique for generating helix-membrane protein folds matching a predefined set of distance constraints, such as those obtained from NMR NOE, chemical cross-linking, dipolar EPR, and FRET experiments. The purpose of the technique is to provide initial structures for local conformational searches based on either energetic considerations or ad-hoc scoring criteria. In order to properly screen the conformational space, the technique generates an exhaustive list of conformations within a specified root-mean-square deviation (RMSD) where the helices are positioned in order to match the provided distances. Our results indicate that the number of structures decreases exponentially as the number of distances increases, and increases exponentially as the errors associated with the distances increases. We also found the number of solutions to be smaller when all the distances share one helix in common, compared to the case where the distances connect helices in a daisy-chain manner. We found that for 7 helices, at least 15 distances with errors up to 8 A are needed to produce a number of solutions that is not too large to be processed by local search refinement procedures. Finally, without energetic considerations, our enumeration technique retrieved the transmembrane domains of Bacteriorhodopsin (PDB entry1c3w), Halorhodopsin (1e12), Rhodopsin (1f88), Aquaporin-1 (1fqy), Glycerol uptake facilitator protein (1fx8), Sensory Rhodopsin (1jgj), and a subunit of Fumarate reductase flavoprotein (1qlaC) with Calpha level RMSDs of 3.0 A, 2.3 A, 3.2 A, 4.6 A, 6.0 A, 3.7 A, and 4.4 A, respectively.
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Affiliation(s)
- Jean-Loup Faulon
- Sandia National Laboratories, PO Box 969, MS 9951, Livermore, CA 94551, USA.
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16
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Goshe MB, Blonder J, Smith RD. Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. J Proteome Res 2003; 2:153-61. [PMID: 12716129 DOI: 10.1021/pr0255607] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to identify and quantitate integral membrane proteins is an analytical challenge for mass spectrometry-based proteomics. The use of surfactants to solubilize and facilitate derivatization of these proteins can suppress peptide ionization and interfere with chromatographic separations during microcapillary reversed-phase liquid chromatography-electrospray-tandem mass spectrometry. To circumvent the use of surfactants and increase proteome coverage, an affinity labeling method has been developed to target highly hydrophobic integral membrane proteins using organic-assisted extraction and solubilization followed by cysteinyl-specific labeling using biotinylation reagents. As demonstrated on the membrane subproteome of Deinococcus radiodurans, specific and quantitative labeling of integral membrane proteins was achieved using a 60% methanol-aqueous buffer system and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine as the cysteinyl-alkylating reagent. From a total of 220 unique Cys-labeled peptides, 89 proteins were identified, of which 40 were integral membrane proteins containing from one to nine mapped transmembrane domains with a maximum positive GRAVY of 1.08. The protocol described can be used with other stable isotope labeling reagents (e.g., ICAT) to enable comparative measurements to be made on differentially expressed hydrophobic membrane proteins from various organisms (e.g., pathogenic bacteria) and cell types and provide a viable method for comparative proteome-wide analyses.
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Affiliation(s)
- Michael B Goshe
- Biological Sciences Division, Pacific Northwest National Laboratory, PO Box 999, MSIN K8-98, Richland, Washington 99352, USA
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17
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Abstract
Bovine rhodopsin is the prototypical G protein coupled receptor (GPCR). It was the first GPCR to be obtained in quantity and studied in detail. It is also the first GPCR for which detailed three dimensional structural information has been obtained. Reviewed here are the experiments leading up to the high resolution structure determination of rhodopsin and the most recent structural information on the activation and stability of this integral membrane protein.
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Affiliation(s)
- Arlene D Albert
- Department of Molecular and Cell Biology, U-125 University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3125, USA
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18
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Gelasco AK, Crouch RK, Knapp DR. Probing the higher order structure of G protein-coupled receptors using tethered cleavage methods. Methods Enzymol 2002; 343:162-70. [PMID: 11665564 DOI: 10.1016/s0076-6879(02)43133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Andrew K Gelasco
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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19
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Knapp DR, Crouch RK, Ball LE, Gelasco AK, Ablonczy Z. Mass spectrometric analysis of G protein-coupled receptors. Methods Enzymol 2002; 343:157-61. [PMID: 11665563 DOI: 10.1016/s0076-6879(02)43132-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Daniel R Knapp
- Department of Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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20
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Ablonczy Z, Kono M, Crouch RK, Knapp DR. Mass spectrometric analysis of integral membrane proteins at the subnanomolar level: application to recombinant photopigments. Anal Chem 2001; 73:4774-9. [PMID: 11681450 DOI: 10.1021/ac015563n] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins produced by eukaryotic expression systems are a subject of much current interest in biomedical investigation. Due to the low efficiency of their expression and the limited quantity of the expressed to the total amount of the membrane proteins, they have evaded mass spectrometric analysis. The methodology previously developed for mass spectrometric analysis of integral membrane proteins required proteins that were obtained relatively pure from their native membranes. The previously developed methodology has been modified and applied to the analysis of subnanomolar samples of rhodopsin. Bovine rhodopsin purified by affinity chromatography, from native membranes and from a eukaryotic expression system, was successfully analyzed, obtaining complete sequence coverage for the detection and localization of posttranslational modifications. The methodology presented here will enable mass spectrometric analysis of subnanomolar levels of photopigments or other integral membrane proteins either from their native membranes or as products of expression systems.
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Affiliation(s)
- Z Ablonczy
- Department of Ophthalmology, Medical University of South Carolina, Charleston 29425, USA
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21
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Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a powerful and widespread analytical tool in all fields of life science. The wide mass range (1-300 kDa), high accuracy, and sensitivity make it a superior method for analysis of all kinds of biomolecules including proteins, nucleic acids, and carbohydrates. In combination with 2D-gelelectrophoresis, MALDI-TOF-MS is particularly suitable for the identification of protein spots via mass fingerprint or microsequencing. Furthermore, the method allows a detailed analysis of posttranslational protein modifications. Recently, the method was also successfully applied to DNA sequencing as well as screening for mutations. Thus, high-throughput genotyping of single nucleotide polymorphisms has the potential to become a routine method for both laboratory and clinical applications.
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Affiliation(s)
- T Bonk
- Institute of Biochemistry, University of Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
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22
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Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1148-1155. [PMID: 11006610 DOI: 10.1002/1096-9888(200009)35:9<1148::aid-jms982>3.0.co;2-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (3 Weeks journals - Search completed at 28th. June 2000)
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