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Ma W, Liu H, Li X. Chemical Synthesis of Peptides and Proteins Bearing Base-Labile Post-Translational Modifications: Evolution of the Methods in Four Decades. Chembiochem 2023; 24:e202300348. [PMID: 37380612 DOI: 10.1002/cbic.202300348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
The S-palmitoylation on Cys residue and O-acetylation on Ser/Thr residues are two types of base-labile post-translational modifications (PTMs) in cells. The lability of these PTMs to bases and nucleophiles makes the peptides/proteins bearing S-palmitoyl or O-acetyl groups challenging synthetic targets, which cannot be prepared via the standard Fmoc-SPPS and native chemical ligation. In this review, we summarized the efforts towards their preparation in the past 40 years, with the focus on the evolution of synthetic methods.
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Affiliation(s)
- Wenjie Ma
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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2
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Kumar N, Bucher D, Kozlowski PM. Mechanistic Implications of Reductive Co–C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase. J Phys Chem B 2019; 123:2210-2216. [DOI: 10.1021/acs.jpcb.8b10820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neeraj Kumar
- Computational Biology and Bioinformatics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Denis Bucher
- Molecular Modeling & Design at leadXpro Villigen, Canton of Aargau, Switzerland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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3
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Li M, Zhai C, Wang S, Huang W, Liu Y, Li Z. Detection of carboxylesterase by a novel hydrosoluble near-infrared fluorescence probe. RSC Adv 2019; 9:40689-40693. [PMID: 35542681 PMCID: PMC9076276 DOI: 10.1039/c9ra08150j] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/03/2019] [Indexed: 01/02/2023] Open
Abstract
A novel hydrosoluble near-infrared fluorescence off–on probe has been developed for detecting carboxylesterase activity.
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Affiliation(s)
- Mengyao Li
- Nutrition & Health Research Institute
- COFCO Corporation
- Beijing Key Laboratory of Nutrition & Health and Food Safety
- Beijing 102209
- China
| | - Chen Zhai
- Nutrition & Health Research Institute
- COFCO Corporation
- Beijing Key Laboratory of Nutrition & Health and Food Safety
- Beijing 102209
- China
| | - Shuya Wang
- Nutrition & Health Research Institute
- COFCO Corporation
- Beijing Key Laboratory of Nutrition & Health and Food Safety
- Beijing 102209
- China
| | - Weixia Huang
- Nutrition & Health Research Institute
- COFCO Corporation
- Beijing Key Laboratory of Nutrition & Health and Food Safety
- Beijing 102209
- China
| | - Yunguo Liu
- College of Life Science and Technology
- Xinjiang University
- Urumqi 830002
- China
| | - Zhao Li
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control
- College of Food Engineering and Nutritional Science
- Shaanxi Normal University
- Xi'an 710062
- China
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5
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Mann D, Güldenhaupt J, Schartner J, Gerwert K, Kötting C. The protonation states of GTP and GppNHp in Ras proteins. J Biol Chem 2018; 293:3871-3879. [PMID: 29382720 DOI: 10.1074/jbc.ra117.001110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/29/2018] [Indexed: 01/09/2023] Open
Abstract
The small GTPase Ras transmits signals in a variety of cellular signaling pathways, most prominently in cell proliferation. GTP hydrolysis in the active center of Ras acts as a prototype for many GTPases and is the key to the understanding of several diseases, including cancer. Therefore, Ras has been the focus of intense research over the last decades. A recent neutron diffraction crystal structure of Ras indicated a protonated γ-guanylyl imidodiphosphate (γ-GppNHp) group, which has put the protonation state of GTP in question. A possible protonation of GTP was not considered in previously published mechanistic studies. To determine the detailed prehydrolysis state of Ras, we calculated infrared and NMR spectra from quantum mechanics/molecular mechanics (QM/MM) simulations and compared them with those from previous studies. Furthermore, we measured infrared spectra of GTP and several GTP analogs bound to lipidated Ras on a membrane system under near-native conditions. Our findings unify results from previous studies and indicate a structural model confirming the hypothesis that γ-GTP is fully deprotonated in the prehydrolysis state of Ras.
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Affiliation(s)
- Daniel Mann
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Jörn Güldenhaupt
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Jonas Schartner
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Klaus Gerwert
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and .,Max-Planck-Gesellschaft-Chinese Academy of Sciences (MPG-CAS) Partner Institute for Computational Biology (PICB), Shanghai 200031, China
| | - Carsten Kötting
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
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6
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Li D, Li Z, Chen W, Yang X. Imaging and Detection of Carboxylesterase in Living Cells and Zebrafish Pretreated with Pesticides by a New Near-Infrared Fluorescence Off-On Probe. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4209-4215. [PMID: 28475833 DOI: 10.1021/acs.jafc.7b00959] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new near-infrared fluorescence off-on probe was developed and applied to fluorescence imaging of carboxylesterase in living HepG-2 cells and zebrafish pretreated with pesticides (carbamate, organophosphorus, and pyrethroid). The probe was readily prepared by connecting (4-acetoxybenzyl)oxy as a quenching and recognizing moiety to a stable hemicyanine skeleton that can be formed via the decomposition of IR-780. The fluorescence off-on response of the probe to carboxylesterase is based on the enzyme-catalyzed spontaneous hydrolysis of the carboxylic ester bond, followed by a further fragmentation of the phenylmethyl unit and thereby the fluorophore release. Compared with the only existing near-infrared carboxylesterase probe, the proposed probe exhibits superior analytical performance, such as near-infrared fluorescence emission over 700 nm as well as high selectivity and sensitivity, with a detection limit of 4.5 × 10-3 U/mL. More importantly, the probe is cell membrane permeable, and its applicability has been successfully demonstrated for monitoring carboxylesterase activity in living HepG-2 cells and zebrafish pretreated with pesticides, revealing that pesticides can effectively inhibit the activity of carboxylesterase. The superior properties of the probe make it of great potential use in indicating pesticide exposure.
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Affiliation(s)
- Dongyu Li
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University , Xi'an 710062, China
| | - Zhao Li
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University , Xi'an 710062, China
| | - Weihua Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Xingbin Yang
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University , Xi'an 710062, China
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7
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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8
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Liu HX, Dang YQ, Yuan YF, Xu ZF, Qiu SX, Tan HB. Diacyl Disulfide: A Reagent for Chemoselective Acylation of Phenols Enabled by 4-(N,N-Dimethylamino)pyridine Catalysis. Org Lett 2016; 18:5584-5587. [DOI: 10.1021/acs.orglett.6b02818] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hong-Xin Liu
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- State
Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial
Key Laboratory of Microbial Culture Collection and Application, Guangdong
Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ya-Qian Dang
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yun-Fei Yuan
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhi-Fang Xu
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Sheng-Xiang Qiu
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hai-Bo Tan
- Program
for Natural Products Chemical Biology, Key Laboratory of Plant Resources
Conservation and Sustainable Utilization, Guangdong Provincial Key
Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Patra S, Erwin N, Winter R. Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes. Chemphyschem 2016; 17:2164-9. [PMID: 27028423 DOI: 10.1002/cphc.201600179] [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: 02/19/2016] [Indexed: 11/07/2022]
Abstract
Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N-Ras and K-Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N-Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K-Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N-Ras forms trimers and K-Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N-Ras trimers and K-Ras dimers as well. The results can be rationalized in terms of the excluded-volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited-hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state-monomeric or clustered-influences their membrane-partitioning behavior and their interplay with cytosolic interaction partners.
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Affiliation(s)
- Satyajit Patra
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Nelli Erwin
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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10
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Chen YX, Koch S, Uhlenbrock K, Weise K, Das D, Gremer L, Brunsveld L, Wittinghofer A, Winter R, Triola G, Waldmann H. Synthesis of the Rheb and K-Ras4B GTPases. Angew Chem Int Ed Engl 2015; 49:6090-5. [PMID: 20652921 DOI: 10.1002/anie.201001884] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yong-Xiang Chen
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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11
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Abstract
One of the main reasons of the high diversity and complexity of the human proteome compared to the human genome is the extensive work performed by the posttranslational machinery to incorporate numerous different functionalities on proteins. The covalent attachment of chemical moieties in proteins after translation is known as posttranslational modification (PTM) and has a crucial role in controlling protein localization and activity. Relevant modifications include phosphorylation, carboxymethylation, glycosylation, acetylation, or lipidation. Despite their essential role on protein function, the synthesis of fully posttranslationally modified proteins has been challenging. However, important advances on chemical biology have enabled the synthesis of fully posttranslationally modified peptides and proteins. As a result of this, peptides bearing, i.e., phosphorylated amino acids, C-terminal methylations, lipid modifications, or nonnatural tags have become accessible. These peptides, as well as the corresponding proteins obtained using ligation techniques, have been invaluable tools in biochemical and biophysical studies. As an example of these advances, this chapter describes the methods developed for the synthesis of lipidated peptides from the Ras and Rab families.
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Affiliation(s)
- Federica Rosi
- Abt. Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Dortmund, Germany
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12
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Werkmüller A, Triola G, Waldmann H, Winter R. Rotational and translational dynamics of ras proteins upon binding to model membrane systems. Chemphyschem 2013; 14:3698-705. [PMID: 24115726 DOI: 10.1002/cphc.201300617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Indexed: 01/16/2023]
Abstract
Plasma-membrane-associated Ras proteins typically control signal transduction processes. As nanoclustering and membrane viscosity sensing provide plausible signaling mechanisms, determination of the rotational and translational dynamics of membrane-bound Ras isoforms can help to link their dynamic mobility to their function. Herein, by using time-resolved fluorescence anisotropy and correlation spectroscopic measurements, we obtain the rotational-correlation time and the translational diffusion coefficient of lipidated boron-dipyrromethene-labeled Ras, both in bulk Ras and upon membrane binding. The results show that the second lipidation motif of N-Ras triggers dimer formation in bulk solution, whereas K-Ras4B is monomeric. Upon membrane binding, an essentially free rotation of the G-domain is observed, along with a high lateral mobility; the latter is essentially limited by the viscosity of the membrane and by lipid-mediated electrostatic interactions. This high diffusional mobility warrants rapid recognition-binding sequences in the membrane-bound state, thereby facilitating efficient interactions between the Ras proteins and scaffolding or effector proteins. The lipid-like rapid lateral diffusion observed here complies with in vivo data.
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Affiliation(s)
- Alexander Werkmüller
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany), Fax: (+49) 231 755 3901
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Kapoor S, Werkmüller A, Goody RS, Waldmann H, Winter R. Pressure modulation of Ras-membrane interactions and intervesicle transfer. J Am Chem Soc 2013; 135:6149-56. [PMID: 23560466 DOI: 10.1021/ja312671j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins attached to the plasma membrane frequently encounter mechanical stresses, including high hydrostatic pressure (HHP) stress. Signaling pathways involving membrane-associated small GTPases (e.g., Ras) have been identified as critical loci for pressure perturbation. However, the impact of mechanical stimuli on biological outputs is still largely terra incognita. The present study explores the effect of HHP on the membrane association, dissociation, and intervesicle transfer process of N-Ras by using a FRET-based assay to obtain the kinetic parameters and volumetric properties along the reaction path of these processes. Notably, membrane association is fostered upon pressurization. Conversely, depending on the nature and lateral organization of the lipid membrane, acceleration or retardation is observed for the dissociation step. In addition, HHP can be inferred as a positive regulator of N-Ras clustering, in particular in heterogeneous membranes. The susceptibility of membrane interaction to pressure raises the idea of a role of lipidated signaling molecules as mechanosensors, transducing mechanical stimuli to chemical signals by regulating their membrane binding and dissociation. Finally, our results provide first insights into the influence of pressure on membrane-associated Ras-controlled signaling events in organisms living under extreme environmental conditions such as those that are encountered in the deep sea and sub-seafloor environments, where pressures reach the kilobar (100 MPa) range.
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Affiliation(s)
- Shobhna Kapoor
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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14
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Güldenhaupt J, Rudack T, Bachler P, Mann D, Triola G, Waldmann H, Kötting C, Gerwert K. N-Ras forms dimers at POPC membranes. Biophys J 2012; 103:1585-93. [PMID: 23062351 DOI: 10.1016/j.bpj.2012.08.043] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/20/2012] [Accepted: 08/23/2012] [Indexed: 12/18/2022] Open
Abstract
Ras is a central regulator of cellular signaling pathways. It is mutated in 20-30% of human tumors. To perform its function, Ras has to be bound to a membrane by a posttranslationally attached lipid anchor. Surprisingly, we identified here dimerization of membrane anchored Ras by combining attenuated total reflectance Fourier transform infrared spectroscopy, biomolecular simulations, and Förster resonance energy transfer experiments. By analyzing x-ray structural models and molecular-dynamics simulations, we propose a dimerization interface between α-helices 4 and 5 and the loop between β2 and β3. This seems to explain why the residues D47, E49, R135, R161, and R164 of this interface are influencing Ras signaling in cellular physiological experiments, although they are not positioned in the catalytic site. Dimerization could catalyze nanoclustering, which is well accepted for membrane-bound Ras. The interface could provide a new target for a seemingly novel type of small molecule interfering with signal transduction in oncogenic Ras mutants.
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Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Bochum, Germany
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15
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The role of G-domain orientation and nucleotide state on the Ras isoform-specific membrane interaction. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:801-13. [PMID: 22851002 DOI: 10.1007/s00249-012-0841-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/26/2012] [Accepted: 07/10/2012] [Indexed: 12/21/2022]
Abstract
Ras proteins are proto-oncogenes that function as molecular switches linking extracellular stimuli with an overlapping but distinctive range of biological outcomes. Although modulatable interactions between the membrane and the Ras C-terminal hypervariable region (HVR) harbouring the membrane anchor motifs enable signalling specificity to be determined by their location, it is becoming clear that the spatial orientation of different Ras proteins is also crucial for their functions. To reveal the orientation of the G-domain at membranes, we conducted an extensive study on different Ras isoforms anchored to model raft membranes. The results show that the G-domain mediates the Ras-membrane interaction by inducing different sets of preferred orientations in the active and inactive states with largely parallel orientation relative to the membrane of most of the helices. The distinct locations of the different isoforms, exposing them to different effectors and regulators, coupled with different G-domain-membrane orientation, suggests synergy between this type of recognition motif and the specificity conferred by the HVR, thereby validating the concept of isoform specificity in Ras.
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16
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Görmer K, Bürger M, Kruijtzer JAW, Vetter I, Vartak N, Brunsveld L, Bastiaens PIH, Liskamp RMJ, Triola G, Waldmann H. Chemical-biological exploration of the limits of the Ras de- and repalmitoylating machinery. Chembiochem 2012; 13:1017-23. [PMID: 22488913 DOI: 10.1002/cbic.201200078] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 11/12/2022]
Abstract
A dynamic de-/repalmitoylation cycle determines localization and activity of H- and N-Ras. This combined cellular de- and repalmitoylation machinery has been shown to be substrate tolerant--it accepts variation of amino acid sequence, structure and configuration. Here, semisynthetic Ras-proteins in which the C-terminal amino acids are replaced by peptoid residues are used to reveal the first limitations of substrate recognition by the de- and repalmitoylating machinery.
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Affiliation(s)
- Kristina Görmer
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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17
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Kötting C, Güldenhaupt J, Gerwert K. Time-resolved FTIR spectroscopy for monitoring protein dynamics exemplified by functional studies of Ras protein bound to a lipid bilayer. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Zhang Y, Chen W, Feng D, Shi W, Li X, Ma H. A spectroscopic off-on probe for simple and sensitive detection ofcarboxylesterase activity and its application to cell imaging. Analyst 2012; 137:716-21. [DOI: 10.1039/c2an15952j] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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Revealing conformational substates of lipidated N-Ras protein by pressure modulation. Proc Natl Acad Sci U S A 2011; 109:460-5. [PMID: 22203965 DOI: 10.1073/pnas.1110553109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulation of protein function is often linked to a conformational switch triggered by chemical or physical signals. To evaluate such conformational changes and to elucidate the underlying molecular mechanisms of subsequent protein function, experimental identification of conformational substates and characterization of conformational equilibria are mandatory. We apply pressure modulation in combination with FTIR spectroscopy to reveal equilibria between spectroscopically resolved substates of the lipidated signaling protein N-Ras. Pressure has the advantage that its thermodynamic conjugate is volume, a parameter that is directly related to structure. The conformational dynamics of N-Ras in its different nucleotide binding states in the absence and presence of a model biomembrane was probed by pressure perturbation. We show that not only nucleotide binding but also the presence of the membrane has a drastic effect on the conformational dynamics and selection of conformational substates of the protein, and a new substate appearing upon membrane binding could be uncovered. Population of this new substate is accompanied by structural reorientations of the G domain, as also indicated by complementary ATR-FTIR and IRRAS measurements. These findings thus illustrate that the membrane controls signaling conformations by acting as an effective interaction partner, which has consequences for the G-domain orientation of membrane-associated N-Ras, which in turn is known to be critical for its effector and modulator interactions. Finally, these results provide insights into the influence of pressure on Ras-controlled signaling events in organisms living under extreme environmental conditions as they are encountered in the deep sea where pressures reach the kbar range.
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Kodela R, Chattopadhyay M, Nath N, Cieciura LZ, Pospishill L, Boring D, Crowell JA, Kashfi K. Synthesis and biological activity of acetyl-protected hydroxybenzyl diethyl phosphates (EHBP) as potential chemotherapeutic agents. Bioorg Med Chem Lett 2011; 21:7146-50. [PMID: 22001089 DOI: 10.1016/j.bmcl.2011.09.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/22/2022]
Abstract
Several acetyl-protected hydroxybenzyl diethyl phosphates (EHBPs) that are capable of forming quinone methide intermediates were synthesized and their cell growth inhibitory properties were evaluated in four different human cancer cell lines. Compounds 1, 1a, and 1b, corresponding to (4-acetyloxybenzyl diethylphosphate), (3-methyl-4-acetyloxybenzyl diethylphosphate), and (3-chloro-4-acetyloxybenzyl diethylphosphate), were significantly more potent than compounds 2 and 3, (2-acetyloxybenzyl diethylphosphate) and (3-acetyloxybenzyl diethylphosphate), respectively. Using HT-29 human colon cancer cells, compounds 1 and 3 increased apoptosis, inhibited proliferation, and caused a G(2)/M block in the cell cycle. Our data suggest that these compounds merit further investigation as potential anti-cancer agents.
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Affiliation(s)
- Ravinder Kodela
- Department of Physiology and Pharmacology, City University of New York Medical School, New York, NY 10031, USA
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Gohlke A, Triola G, Waldmann H, Winter R. Influence of the lipid anchor motif of N-ras on the interaction with lipid membranes: a surface plasmon resonance study. Biophys J 2010; 98:2226-35. [PMID: 20483331 DOI: 10.1016/j.bpj.2010.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 01/30/2010] [Accepted: 02/02/2010] [Indexed: 10/19/2022] Open
Abstract
Ras GTPases play a crucial role in signal transduction cascades involved in cell differentiation and proliferation, and membrane binding is essential for their proper function. To determine the influence of the nature of the lipid anchor motif and the difference between the active (GTP) and inactive (GDP) forms of N-Ras on partitioning and localization in the lipid membrane, five different N-Ras constructs with different lipid anchors and nucleotide loading (Far/Far (GDP), HD/Far (GDP), HD/HD (GDP), Far (GDP), and HD/Far (GppNHp)) were synthesized. Using the surface plasmon resonance technique, we were able to follow the insertion and dissociation process of the lipidated proteins into and out of model membranes consisting of pure liquid-ordered (l(o)) or liquid-disordered (l(d)) phase and a heterogeneous two-phase mixture, i.e., a raft mixture with l(o) + l(d) phase coexistence. In addition, we examined the influence of negatively charged headgroups and stored curvature elastic stress on the binding properties of the lipidated N-Ras proteins. In most cases, significant differences were found for the various anchor motifs. In general, N-Ras proteins insert preferentially into a fluidlike, rather than a rigid, ordered lipid bilayer environment. Electrostatic interactions with lipid headgroups or stored curvature elastic stress of the membrane seem to have no drastic effect on the binding and dissociation processes of the lipidated proteins. The monofarnesylated N-Ras exhibits generally the highest association rate and fastest dissociation process in fluidlike membranes. Double lipidation, especially including farnesylation, of the protein leads to drastically reduced initial binding rates but strong final association. The change in the nucleotide loading of the natural N-Ras HD/Far induces a slightly different binding and dissociation kinetics, as well as stability of association, and seems to influence the tendency to segregate laterally in the membrane plane. The GDP-bound inactive form of N-Ras with an HD/Far anchor shows stronger membrane association, which might be due to a more pronounced tendency to self-assemble in the membrane matrix than is seen with the active GTP-bound form.
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Affiliation(s)
- Andrea Gohlke
- Faculty of Chemistry, Physical Chemistry I-Biophysical Chemistry, Technische Universität Dortmund, Dortmund, Germany
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Chen YX, Koch S, Uhlenbrock K, Weise K, Das D, Gremer L, Brunsveld L, Wittinghofer A, Winter R, Triola G, Waldmann H. Synthesis of the Rheb and K-Ras4B GTPases. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001884] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Triola G, Gerauer M, Görmer K, Brunsveld L, Waldmann H. Solid-Phase Synthesis of Lipidated Ras Peptides Employing the Ellman Sulfonamide Linker. Chemistry 2010; 16:9585-91. [DOI: 10.1002/chem.201001642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Vogel A, Reuther G, Roark MB, Tan KT, Waldmann H, Feller SE, Huster D. Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:275-85. [DOI: 10.1016/j.bbamem.2009.09.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 09/28/2009] [Accepted: 09/30/2009] [Indexed: 10/20/2022]
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25
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Ludolph B, Waldmann H. Solid-phase synthesis of benzodiazepinediones mimicking the C-terminus of the H-Ras protein. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Güldenhaupt J, Adigüzel Y, Kuhlmann J, Waldmann H, Kötting C, Gerwert K. Secondary structure of lipidated Ras bound to a lipid bilayer. FEBS J 2009; 275:5910-8. [PMID: 19021766 DOI: 10.1111/j.1742-4658.2008.06720.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ras proteins are small guanine nucleotide binding proteins that regulate many cellular processes, including growth control. They undergo distinct post-translational lipid modifications that are required for appropriate targeting to membranes. This, in turn, is critical for Ras biological function. However, most in vitro studies have been conducted on nonlipidated truncated forms of Ras proteins. Here, for the first time, attenuated total reflectance-FTIR studies of lipid-modified membrane-bound N-Ras are performed, and compared with nonlipidated truncated Ras in solution. For these studies, lipidated N-Ras was prepared by linking a farnesylated and hexadecylated N-Ras lipopeptide to a truncated N-Ras protein (residues 1-181). It was then bound to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer tethered on an attenuated total reflectance crystal. The structurally sensitive amide I absorbance band in the IR was detected and analysed to determine the secondary structure of the protein. The NMR three-dimensional structure of truncated Ras was used to calibrate the contributions of the different secondary structural elements to the amide I absorbance band of truncated Ras. Using this novel approach, the correct decomposition was selected from several possible solutions. The same parameter set was then used for the membrane-bound lipidated Ras, and provided a reliable decomposition for the membrane-bound form in comparison with truncated Ras. This comparison indicates that the secondary structure of membrane-bound Ras is similar to that determined for the nonlipidated truncated Ras protein for the highly conserved G-domain. This result validates the multitude of investigations of truncated Ras without anchor in vitro. The novel attenuated total reflectance approach opens the way for detailed studies of the interaction network of the membrane-bound Ras protein.
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Weise K, Triola G, Brunsveld L, Waldmann H, Winter R. Influence of the Lipidation Motif on the Partitioning and Association of N-Ras in Model Membrane Subdomains. J Am Chem Soc 2009; 131:1557-64. [DOI: 10.1021/ja808691r] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katrin Weise
- Physical Chemistry I - Biophysical Chemistry and Chemical Biology, Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Straβe 6, D-44227 Dortmund, Germany and Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straβe 11, D-44227 Dortmund, Germany
| | - Gemma Triola
- Physical Chemistry I - Biophysical Chemistry and Chemical Biology, Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Straβe 6, D-44227 Dortmund, Germany and Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straβe 11, D-44227 Dortmund, Germany
| | - Luc Brunsveld
- Physical Chemistry I - Biophysical Chemistry and Chemical Biology, Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Straβe 6, D-44227 Dortmund, Germany and Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straβe 11, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- Physical Chemistry I - Biophysical Chemistry and Chemical Biology, Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Straβe 6, D-44227 Dortmund, Germany and Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straβe 11, D-44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry and Chemical Biology, Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Straβe 6, D-44227 Dortmund, Germany and Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straβe 11, D-44227 Dortmund, Germany
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Brunsveld L, Waldmann H, Huster D. Membrane binding of lipidated Ras peptides and proteins--the structural point of view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:273-88. [PMID: 18771652 DOI: 10.1016/j.bbamem.2008.08.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
Abstract
Biological membranes are interesting interfaces, at which important biological processes occur. In addition to integral membrane proteins, a number of proteins bind to the membrane surface and associate with it. Posttranslational lipid modification is one important mechanism, by which soluble molecules develop a propensity towards the membrane and reversibly bind to it. Membrane binding by insertion of hydrophobic lipid moieties is relevant for up to 10% of all cellular proteins. A particular interesting lipid-modified protein is the small GTPase Ras, which plays a key role in cellular signal transduction. Until recently, the structural basis for membrane binding of Ras was not well-defined. However, with the advent of new synthesis techniques and the advancement of several biophysical methods, a number of structural and dynamical features about membrane binding of Ras proteins have been revealed. This review will summarize the chemical biology of Ras and discuss in more detail the biophysical and structural features of the membrane bound C-terminus of the protein.
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Affiliation(s)
- Luc Brunsveld
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
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29
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Vogel A, Tan KT, Waldmann H, Feller SE, Brown MF, Huster D. Flexibility of ras lipid modifications studied by 2H solid-state NMR and molecular dynamics simulations. Biophys J 2007; 93:2697-712. [PMID: 17557790 PMCID: PMC1989704 DOI: 10.1529/biophysj.107.104562] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human posttranslationally modified N-ras oncogenes are known to be implicated in numerous human cancers. Here, we applied a combination of experimental and computational techniques to determine structural and dynamical details of the lipid chain modifications of an N-ras heptapeptide in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes. Experimentally, 2H NMR spectroscopy was used to study oriented membranes that incorporated ras heptapeptides with two covalently attached perdeuterated hexadecyl chains. Atomistic molecular dynamics simulations of the same system were carried out over 100 ns including 60 DMPC and 4 ras molecules. Several structural and dynamical experimental parameters could be directly compared to the simulation. Experimental and simulated 2H NMR order parameters for the methylene groups of the ras lipid chains exhibited a systematic difference attributable to the absence of collective motions in the simulation and to geometrical effects. In contrast, experimental 2H NMR spin-lattice relaxation rates for Zeeman order were well reproduced in the simulation. The lack of slower collective motions in the simulation did not appreciably influence the relaxation rates at a Larmor frequency of 115.1 MHz. The experimental angular dependence of the 2H NMR relaxation rates with respect to the external magnetic field was also relatively well simulated. These relaxation rates showed a weak angular dependence, suggesting that the lipid modifications of ras are very flexible and highly mobile in agreement with the low order parameters. To quantify these results, the angular dependence of the 2H relaxation rates was calculated by an analytical model considering both molecular and collective motions. Peptide dynamics in the membrane could be modeled by an anisotropic diffusion tensor with principal values of Dparallel=2.1x10(9) s(-1) and Dperpendicular=4.5x10(5) s(-1). A viscoelastic fitting parameter describing the membrane elasticity, viscosity, and temperature was found to be relatively similar for the ras peptide and the DMPC host matrix. Large motional amplitudes and relatively short correlation times facilitate mixing and dispersal with the lipid bilayer matrix, with implications for the role of the full-length ras protein in signal transduction and oncogenesis.
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Affiliation(s)
- Alexander Vogel
- Junior Research Group Structural Biology of Membrane Proteins, Institute of Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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Vogel A, Katzka CP, Waldmann H, Arnold K, Brown MF, Huster D. Lipid Modifications of a Ras Peptide Exhibit Altered Packing and Mobility versus Host Membrane as Detected by 2H Solid-State NMR. J Am Chem Soc 2005; 127:12263-72. [PMID: 16131204 DOI: 10.1021/ja051856c] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human N-ras protein binds to cellular membranes by insertion of two covalently bound posttranslational lipid modifications, which is crucial for its function in signal transduction and cell proliferation. Mutations in ras may lead to unregulated cell growth and eventually cancer, making it an important therapeutic target. Here we have investigated the molecular details of the membrane binding mechanism. A heptapeptide derived from the C-terminus of the human N-ras protein was synthesized including two hexadecyl modifications. Solid-state 2H NMR was used to determine the packing and molecular dynamics of the ras lipid chains as well as the phospholipid matrix. Separately labeling the chains of the peptide and the phospholipids with 2H enabled us to obtain atomically resolved parameters relevant to their structural dynamics. While the presence of ras only marginally affected the packing of DMPC membranes, dramatically lower order parameters (S(CD)) were observed for the ras acyl chains indicating modified packing properties. Essentially identical projected lengths of the 16:0 ras chains and the 14:0 DMPC chains were found, implying that the polypeptide backbone is located at the lipid-water interface. Dynamical properties of both the ras and phospholipid chains were determined from spin-lattice 2H relaxation (R1Z) measurements. Plots of R1Z rates versus the corresponding squared segmental order parameters revealed striking differences. We propose the ras peptide is confined to microdomains containing DMPC chains which are in exchange with the bulk bilayer on the 2H NMR time scale (approximately 10(-5) s). Compared to the host DMPC matrix, the ras lipid modifications are extremely flexible and undergo relatively large amplitude motions. It is hypothesized that this flexibility is a requirement for the optimal anchoring of lipid-modified proteins to cellular membranes.
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Affiliation(s)
- Alexander Vogel
- Biotechnological-Biomedical Center of the University of Leipzig, D-04107 Leipzig, Germany
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31
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Wen SJ, Hu TS, Yao ZJ. Macrocyclization studies and total synthesis of cyclomarin C, an anti-inflammatory marine cyclopeptide. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.03.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Gorfe AA, Pellarin R, Caflisch A. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J Am Chem Soc 2005; 126:15277-86. [PMID: 15548025 DOI: 10.1021/ja046607n] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipid-modified membrane-binding proteins are essential in signal transduction events of the cell, a typical example being the GTPase ras. Recently, membrane binding of a doubly lipid-modified heptapeptide from the C-terminus of the human N-ras protein was studied by spectroscopic techniques. It was found that membrane binding is mainly due to lipid chain insertion, but it is also favored by interactions between apolar side chains and the hydrophobic region of the membrane. Here, 10 explicit solvent molecular dynamics simulations for a total time of about 150 ns are used to investigate the atomic details of the peptide-membrane association. The 16:0 peptide lipid chains are more mobile than the 14:0 phospholipid chains, which is in agreement with (2)H NMR experiments. Peptide-lipid and peptide-solvent interactions, backbone and side-chain distributions, as well as the effects of lipidated peptide insertion onto the structure, and dynamics of a 1,2-dimyristoylglycero-3-phosphocholine bilayer are described. The simulation results validate the structural model proposed by the analysis of spectroscopic data and highlight the main aspects of the insertion mechanism. The peptide in the membrane is rather rigid over the simulation time scale of about 10 ns, but different partially extended conformations devoid of backbone hydrogen bonds are observed in different trajectories.
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Affiliation(s)
- Alemayehu A Gorfe
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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33
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Somers NA, Kazlauskas RJ. Mapping the substrate selectivity and enantioselectivity of esterases from thermophiles. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.07.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Huster D, Vogel A, Katzka C, Scheidt HA, Binder H, Dante S, Gutberlet T, Zschörnig O, Waldmann H, Arnold K. Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy. J Am Chem Soc 2003; 125:4070-9. [PMID: 12670227 DOI: 10.1021/ja0289245] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane binding of a doubly lipid modified heptapeptide from the C-terminus of the human N-ras protein was studied by Fourier transform infrared, solid-state NMR, and neutron diffraction spectroscopy. The 16:0 peptide chains insert well into the 1,2-dimyristoyl-sn-glycero-3-phosphocholine phospholipid matrix. This is indicated by a common main phase transition temperature of 21.5 degrees C for both the lipid and peptide chains as revealed by FTIR measurements. Further, (2)H NMR reveals that peptide and lipid chains have approximately the same chain length in the liquid crystalline state. This is achieved by a much lower order parameter of the 16:0 peptide chains compared to the 14:0 phospholipid chains. Finally, proton/deuterium contrast variation of neutron diffraction experiments indicates that peptide chains are localized in the membrane interior analogous to the phospholipid chains. In agreement with this model of peptide chain insertion, the peptide part is localized at the lipid-water interface of the membrane. This is revealed by (1)H nuclear Overhauser enhancement spectra recorded under magic angle spinning conditions. Quantitative cross-peak analysis allows the examination of the average location of the peptide backbone and side chains with respect to the membrane. While the backbone shows the strongest cross-relaxation rates with the phospholipid glycerol, the hydrophobic side chains of the peptide insert deeper into the membrane interior. This is supported by neutron diffraction experiments that reveal a peptide distribution in the lipid-water interface of the membrane. Concurring with these experimental findings, the amide protons of the peptide show strong water exchange as seen in NMR and FTIR measurements. No indications for a hydrogen-bonded secondary structure of the peptide backbone are found. Therefore, membrane binding of the C-terminus of the N-ras protein is mainly due to lipid chain insertion but also supported by interactions between hydrophobic side chains and the lipid membrane. The peptide assumes a mobile and disordered conformation in the membrane. Since the C-terminus of the soluble part of the ras protein is also disordered, we hypothesize that our model for membrane binding of the ras peptide realistically describes the membrane binding of the lipidated C-terminus of the active ras protein.
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Affiliation(s)
- Daniel Huster
- Junior Research Group Solid-state NMR Studies of Membrane-associated Proteins, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany.
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35
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Greenwald RB, Choe YH, McGuire J, Conover CD. Effective drug delivery by PEGylated drug conjugates. Adv Drug Deliv Rev 2003; 55:217-50. [PMID: 12564978 DOI: 10.1016/s0169-409x(02)00180-1] [Citation(s) in RCA: 640] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The current review presents an update of drug delivery using poly(ethylene glycol) (PEG), that focuses on recent developments in both protein and organic drugs. Certainly the past 10 years has resulted in a renaissance of the field of PEG drug conjugates, initiated by the use of higher molecular weight PEGs (M(w)>20,000), especially 40,000 which is estimated to have a plasma circulating t(1/2) of approximately 10 h in mice. This recent resuscitation of small organic molecule delivery by high molecular weight PEG conjugates was founded on meaningful in vivo testing using established tumor models, and has led to a clinical candidate, PEG-camptothecin (PROTHECAN), an ester based prodrug currently in phase II trials. Additional applications of high molecular weight PEG prodrug strategies to amino containing drugs are presented: similar tripartate systems based on lower M(w) PEG and their use with proteins is expounded on. The modification of a benzyl elimination tripartate prodrug specific for mercaptans is presented, and its successful application to 6-mercaptopurine giving a water soluble formulation is discussed. Recent novel PEG oligonucleotides and immunoconjugates are also covered. Clinical results of FDA approved PEGylated proteins are also presented.
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36
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Chen ZZ, Li YM, Zhao YF. Hydrolysis of Dipeptide N-Heptyl Esters with Newlase F. JOURNAL OF CHEMICAL RESEARCH 2003. [DOI: 10.3184/030823403103172779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Newlase F, a crude enzyme containing lipase and protease, can be used in the synthesis of peptide conjugates; the hydrolysis conditions were optimized to increase lipase activity and suppress protease activity and in addition, N-terminal protecting groups and peptide bonds were not affected.
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Affiliation(s)
- Zhong-Zhou Chen
- Bioorganic Phosphorus Chemistry Laboratory, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yan-Mei Li
- Bioorganic Phosphorus Chemistry Laboratory, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yu-Fen Zhao
- Bioorganic Phosphorus Chemistry Laboratory, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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37
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Völkert M, Koul S, Müller GH, Lehnig M, Waldmann H. Phenylhydrazide as an enzyme-labile protecting group in peptide synthesis. J Org Chem 2002; 67:6902-10. [PMID: 12353981 DOI: 10.1021/jo0259966] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enzymatic cleavage of amino acid phenylhydrazides with the enzyme tyrosinase (EC 1.14.18.1) offers a new, mild, and selective method for C-terminal deprotection of peptides. The advantages of the described methodology are the very mild oxidative removal of the protecting group at room temperature and pH 7, a high chemo- and regioselectivity, and the availability of the biocatalyst. Even in oxygen-saturated solution, the oxidation of sensitive methionine residues was not observed. These features make the methodology suitable for the synthesis of sensitive peptide conjugates. Mechanistic data suggest that the hydrolysis of the oxidized adducts proceeds by a free-radical mechanism.
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Affiliation(s)
- Martin Völkert
- Department of Chemical Biology, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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38
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Chen ZZ, Li YM, Peng X, Huang FR, Zhao YF. The use of crude lipase in deprotection of C-terminal protecting groups. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1381-1177(02)00102-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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39
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Abstract
Characteristic partial structures of lipidated proteins embodying different lipid groups as well as additional fluorescent tags or a maleimide for coupling to proteins can be synthesized readily by means of a new solid-phase technique employing the oxidative cleavage of the hydrazide linker as well as on-resin farnesylation and palmitoylation after appropriate deprotection of cysteine thiol groups as the key steps.
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Affiliation(s)
- Björn Ludolph
- Max-Planck-Institut für molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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40
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Creaser SP, Peterson BR. Sensitive and rapid analysis of protein palmitoylation with a synthetic cell-permeable mimic of SRC oncoproteins. J Am Chem Soc 2002; 124:2444-5. [PMID: 11890786 DOI: 10.1021/ja017671x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The localization of oncogenic Src and Ras proteins to cellular plasma membranes is critical for the proliferation of specific cancers. In addition to other lipid modifications, these proteins require posttranslational palmitoylation of specific cysteine residues by the enzyme palmitoyl acyltransferase (PAT) in order to be stably anchored at plasma membranes. Hence, the identification of inhibitors of protein palmitoylation has significant potential to define a new class of antitumor agents. However, studies of protein palmitoylation have been hindered by the dynamic and reversible nature of cysteine acylation and the lack of sensitive and convenient assays of PAT activity. To facilitate the rapid identification of compounds that affect protein palmitoylation, we report the solid-phase synthesis of a fluorescent cell-permeable palmitoyl acyltransferase substrate that mimics the N-terminus of Src family proteins. Metabolic radiolabeling and epifluorescence microscopy of Jurkat lymphocytes treated with this Src-mimetic lipopeptide revealed that this compound is palmitoylated intracellularly, which confers localization at cellular plasma membranes. Addition of the palmitoylation inhibitor 2-bromopalmitic acid to substrate-treated cells blocked palmitoylation and diminished substrate-mediated plasma membrane fluorescence. Analysis of inhibition of palmitoylation by flow cytometry revealed that this fluorescent lipopeptide substrate represents a highly sensitive molecular probe of palmitoyl acyltransferase activity that enables unprecedented high-throughput assays of protein palmitoylation.
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Affiliation(s)
- Steffen P Creaser
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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41
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Lipidated peptides as tools for understanding the membrane interactions of lipid-modified proteins. PEPTIDE-LIPID INTERACTIONS 2002. [DOI: 10.1016/s1063-5823(02)52015-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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42
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Affiliation(s)
- D Kadereit
- Institut für Organische Chemie, Universität Karlsruhe, Richard-Willstätter-Allee 2, D-76128 Karlsruhe, Germany
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Abstract
In this review, we summarize the successful interplay between three disciplines, organic synthesis, biophysics and cell biology, in the study of protein lipidation and its relevance to targeting of proteins to the plasma membrane of cells in molecular detail. Highlighting the example of the Ras proteins, we show how the development of new synthetic methodologies paved the road to the synthesis of lipidated peptides and--by a combination of chemical and molecular biological techniques--lipidated proteins as molecular tools. We further give an overview of the results of the biophysical properties and biological activities of the molecules synthesized by means of this interdisciplinary approach. This successful combination of different disciplines led to a better understanding of the selective targeting of Ras and related lipoproteins to the plasma membrane.
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Affiliation(s)
- M Völkert
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany
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44
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Zhu Y, van der Donk WA. Convergent Synthesis of Peptide Conjugates Using Dehydroalanines for Chemoselective Ligations. Org Lett 2001; 3:1189-92. [PMID: 11348191 DOI: 10.1021/ol015648a] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text]. Protein and peptide conjugates such as glycopeptides, prenylated peptides, and lipopeptides play essential roles in biology. A rapid and convergent entry into a variety of these compounds is described. The methodology involves the introduction of a dehydroalanine into peptides and subsequent chemoselective conjugate addition of an appropriate thiolate nucleophile, including farnesylthiolate or thioglycosides.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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45
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Seitz O, Heinemann I, Mattes A, Waldmann H. Synthetic peptide conjugates—tailor-made probes for the biology of protein modification and protein processing. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)01115-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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46
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Lee S, Greenwald RB, McGuire J, Yang K, Shi C. Drug delivery systems employing 1,6-elimination: releasable poly(ethylene glycol) conjugates of proteins. Bioconjug Chem 2001; 12:163-9. [PMID: 11312676 DOI: 10.1021/bc000064z] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using lysozyme as a representative protein substrate that loses its activity when PEGylation takes place on the epsilon-amino group of lysine residues, various amounts of a novel releasable PEG linker (rPEG) were conjugated to the protein. rPEG-lysozyme conjugates were relatively stable in pH 7.4 buffer for over 24 h. However, regeneration of native protein from the rPEG conjugates occurred in a predictable manner during incubation in high pH buffer or rat plasma, as demonstrated by enzymatic activity and structural characterization. The rates of regeneration were also correlated with PEG number: native lysozyme was released more rapidly from the monosubstituted conjugate than from the disubstituted conjugate, suggesting possible steric hindrance to the approach of cleaving enzymes. Recovery of normal activity and structure for the regenerated native lysozyme was shown by a variety of assays.
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Affiliation(s)
- S Lee
- Enzon, Inc., 20 Kingsbridge Road, Piscataway, New Jersey 08854, USA.
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47
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Kuhn K, Owen DJ, Bader B, Wittinghofer A, Kuhlmann J, Waldmann H. Synthesis of functional Ras lipoproteins and fluorescent derivatives. J Am Chem Soc 2001; 123:1023-35. [PMID: 11456655 DOI: 10.1021/ja002723o] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the study of biological signal transduction, access to correctly lipidated proteins is of utmost importance. Furthermore, access to bioconjugates that embody the correct structure of the protein but that may additionally carry different lipid groups or labels (i.e., fluorescent tags) by which the protein can be traced in biological systems, could provide invaluable reagents. We report here of the development of techniques for the synthesis of a series of modified Ras proteins. These modified Ras proteins carry a number of different, natural and non-natural lipid residues, and the process was extended to also provide access to a number of fluorescently labeled derivatives. The maleimide group provided the key to link chemically synthesized lipopeptide molecules in a specific and efficient manner to a truncated form of the H-Ras protein. Furthermore, a preliminary study on the biological activity of the natural Ras protein derivative (containing the normal farnesyl and palmitoyl lipid residues) has shown full biological activity. This result highlights the usefulness of these compounds as invaluable tools for the study of Ras signal transduction processes and the plasma membrane localization of the Ras proteins.
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Affiliation(s)
- K Kuhn
- Department of Chemical Biology, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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48
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Bonnet D, Ollivier N, Gras-Masse H, Melnyk O. Chemoselective acylation of fully deprotected hydrazino acetyl peptides. Application to the synthesis of lipopetides. J Org Chem 2001; 66:443-9. [PMID: 11429812 DOI: 10.1021/jo0010577] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fully deprotected N-terminal alpha-hydrazino acetyl peptides were synthesized and chemoselectively acylated on the hydrazine moiety with various fatty acid succinimidyl esters or N-(cholesterylcarbonyloxy) succinimide to give lipopeptides of high purity. The buffer and pH were adjusted in order to minimize the oxidation of the hydrazine moiety and to achieve the best conversion and selectivity. The acylation was performed in a citrate-phosphate buffer/2-methylpropan-2-ol mixture of pH 5.1. The pKa of the alpha-hydrazino acetyl group on our model peptide was found to be 6.45, i.e., about 2 units lower than the pKa of a glycyl residue. The reaction was subsequently applied to the synthesis of a 38AA peptide derivatized by a palmitoyl group.
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Affiliation(s)
- D Bonnet
- UMR 8525 CNRS-Institut Pasteur de Lille-Université de Lille 2, Institut de Biologie de Lille, 1 rue du Professeur Calmette 59019 Lille, France
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49
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Eisele F, Kuhlmann J, Waldmann H. Synthesis and Membrane-Binding Properties of a Characteristic Lipopeptide from the Membrane-Anchoring Domain of Influenza Virus A Hemagglutinin. Angew Chem Int Ed Engl 2001; 40:369-373. [PMID: 29712417 DOI: 10.1002/1521-3773(20010119)40:2<369::aid-anie369>3.0.co;2-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2000] [Indexed: 11/06/2022]
Abstract
On the trail of the influenza virus! Fluorescent-labeled lipopeptides, such as the characteristic S-palmitoylated partial structure from influenza virus hemagglutinin A, can be synthesized efficiently by employing a new enzymatic protecting-group technique in the key steps. Their binding to model membranes was determined in a kinetic assay, so leading to a first approximation of the membrane-anchoring ability of the corresponding lipopeptide motif in the parent protein.
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Affiliation(s)
- Frank Eisele
- Universität Karlsruhe Institut für Organische Chemie Richard-Willstätter-Allee 2, 76128 Karlsruhe (Germany)
| | - Jürgen Kuhlmann
- Max-Planck-Institut für molekulare Physiologie Abteilung Strukturelle Biologie Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
| | - Herbert Waldmann
- Max-Planck-Institut für molekulare Physiologie Abteilung Chemische Biologie and Universität Dortmund Institut für Organische Chemie Otto-Hahn-Strasse 11, 44227 Dortmund (Germany) Fax: (+49) 231-133-2499
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50
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Eisele F, Kuhlmann J, Waldmann H. Synthese und Membranbindungseigenschaften eines Lipopeptids der membranassoziierten Domäne des Influenza-A-Virus-Hämagglutinins. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010119)113:2<382::aid-ange382>3.0.co;2-f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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