The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy

Many proteins involved in signal transduction are equipped with covalently attached lipid chains providing a hydrophobic anchor targeting these molecules to membranes. Despite the considerable biological significance of this membrane binding mechanism for 5-10% of all cellular proteins, to date very little is known about structural and dynamical features of lipidated membrane binding domains. Here we report the first comprehensive study of the molecular dynamics of the C-terminus of membrane-associated full-length lipidated Ras protein determined by solid-state NMR. Fully functional lipid-modified N-Ras protein was obtained by chemical-biological synthesis ligating the expressed water soluble N-terminus with a chemically synthesized (2)H or (13)C labeled lipidated heptapeptide. Dynamical parameters for the lipid chain modification at Cys 181 were determined from static (2)H NMR order parameter and relaxation measurements. Order parameters describing the amplitude of motion in the protein backbone and the side chain were determined from site-specific measurements of (1)H-(13)C dipolar couplings for all seven amino acids in the membrane anchor of Ras. Finally, the correlation times of motion were determined from temperature dependent relaxation time measurements and analyzed using a modified Lipari Szabo approach. Overall, the C-terminus of Ras shows a versatile dynamics with segmental fluctuations and axially symmetric overall motions on the membrane surface. In particular, the lipid chain modifications are highly flexible in the membrane.     

Visualizing association of N-ras in lipid microdomains: influence of domain structure and interfacial adsorption

In this study, two-photon fluorescence microscopy on giant unilamellar vesicles and tapping-mode atomic force microscopy (AFM) are applied to follow the insertion of a fluorescently (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, BODIPY) labeled and completely lipidated (hexadecylated and farnesylated) N-Ras protein into heterogeneous lipid bilayer systems. The bilayers consist of the canonical raft mixture 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol, which-depending on the concentration of the constituents-separates into liquid-disordered (l(d)), liquid-ordered (l(o)), and solid-ordered (s(o)) phases. The results provide direct evidence that partitioning of N-Ras occurs preferentially into liquid-disordered lipid domains, which is also reflected in a faster kinetics of incorporation into the fluid lipid bilayers. The phase sequence of preferential binding of N-Ras to mixed-domain lipid vesicles is l(d) > l(o) > s(o). Intriguingly, we detect, using the better spatial resolution of AFM, also a large proportion of the lipidated protein located at the l(d)/l(o) phase boundary, thus leading to a favorable decrease in line tension that is associated with the rim of the demixed phases. Such an interfacial adsorption effect may serve as an alternative vehicle for association processes of signaling proteins in membranes.     

Synthetic Strategies for Artificial Lipidation of Functional Proteins

Biosynthesis of natural lipidated proteins is linked to important signal pathways, and therefore analyzing protein lipidation is crucial for understanding cellular functions. Artificial lipidation of proteins has attracted attention in recent decades as it allows modulation of the amphiphilic nature of the protein of interest, and is used in the design of drug-delivery systems containing antibodies anchored on a lipid bilayer carrier. However, the intrinsic hydrophobicity of lipids makes the synthesis of lipid–protein conjugates challenging with respect to the yield and selectivity of the lipidation. In this Minireview, the development of chemical and enzymatic synthetic strategies for the preparation of a range of lipid–protein conjugates that do not compromise the functions of the proteins are discussed as well as applications of the conjugates.     

脂蛋白合成新进展

生物体内的信号传导蛋白在膜上的定位与其生物功能的发挥依赖于特定脂肪链的修饰,然而传统的基因表达法合成脂蛋白,得到的纯品产率很低.在近10年中,逐渐发展起来一种新的合成方法,即将化学合成脂修饰的多肽与基因表达培养蛋白相结合,可以合成出具有多条脂肪链修饰的蛋白缀合物,并且整个合成过程在非常温和的环境中进行,产品能保持较高的纯度和活性.采用该方法合成的脂蛋白用于体外的实验中,其结果与生物体内的现象非常接近.脂蛋白合成方法的发展对研究细胞中的信号传导过程具有重要的意义,并在药物合成和提高药效方面都有很多应用,这对于研究恶性肿瘤等疾病的发病机理起到了重要的推动作用.同时该脂蛋白合成的成功是采用化学法合成生物大分子解释生物体内的现象一个重大的突破,是化学生物学发展重要的一步.     

Exploring enzymatic catalysis at a solid surface: a case study with transglutaminase-mediated protein immobilization

The factors affecting enzymatic protein immobilization with microbial transglutaminase (MTG) were explored. As model proteins, enhanced green fluorescent protein (EGFP) and glutathione S-transferase (GST) were chosen and tagged with a neutral Gln-donor substrate peptide for MTG (Leu-Leu-Gln-Gly, LLQG-tag) at their C-terminus. To create a specific surface, displaying reactive Lys residues, to be cross-linked with the Gln residue in the LLQG-tag of target proteins by MTG catalysis, a polystyrene surface was physically coated with beta-casein. Both recombinant proteins were immobilized onto the beta-casein-coated surface only in the presence of active MTG, indicating that those proteins were enzymatically immobilized to the surface. MTG-mediated protein immobilization markedly depends on the pH and ionic strength of the reaction media. The optimal pH range of MTG-mediated immobilization of both recombinant proteins was around 5, at which point the MTG-catalyzed reaction in aqueous solution is not normally preferred. By utilizing a pH-dependent change in EGFP fluorescence, we found that the apparent pH at the surface is likely to be lower than bulk pH, this difference is not attributed to an optimal pH shift in MTG-mediated immobilization. On the other hand, lower yields of protein immobilization at higher ionic strength suggest that electrostatic interaction is a key factor governing MTG catalysis at a solid surface. The results of this study indicate that, in enzymatic catalysis at a solid surface, the concentration of substrates at the surface can enhance the catalytic efficiency, and this could alter the pH dependence of enzymatic catalysis.     

Molecular activities and ligand-binding specificities of StAR-related lipid transfer domains: exploring integrated in silico methods and ensemble-docking approaches

In this study, cholesterol biotransformation gene-set of human steroidogenic acute regulatory protein-related lipid transfer (START) domains were evaluated from high-throughput gene screening approaches. It was shown that STARD1, STARD3 and STARD4 proteins are better effective transporters of cholesterol than STARD5 and STARD6 domains. Docking studies show a strong agreement with gene ontology enrichment data. According to both complementary strategies, it was found that only STARD1, STARD3 and STARD4 are potentially involved in cholesterol biotransformation in mitochondria through Ω1-loop of C-terminal α4-helical domain. Ensemble docking assessment for a set of selected chemicals of protein–chemical networks has shown possible binding probabilities with START domains. Among those, reproductive toxicity evoked drugs (mifepristone), insecticides (rotenone), tobacco pulmonary carcinogens (benzo(a)pyrene) and endocrine disruptor chemicals (EDCs) including perfluorooctanesulfonic acid (PFOS) and aflatoxin B₁ (AFB₁) potentially bound with novel hotspot residues of the α4-helical domain. Compound representation space and clustering approaches reveal that the START proteins show more sensitivity with these lead scaffolds, so they could provide probable barrier assets in cholesterol and steroidogenic acute regulatory (StAR) binding and leads adverse consequences in steroidogenesis. These findings indicate potential START domains and their binding levels with toxic chemicals; sorted viewpoints could be useful as a promising way to identify chemicals with related steroidogenisis impacts on human health.     

Synthesis of lipidated green fluorescent protein and its incorporation in supported lipid bilayers

Herein we report a semisynthetic method of producing membrane-anchored proteins. Ligation of synthetic lipids with designed anchor structures to proteins was performed using native chemical ligation (NCL) of a C-terminal peptide thioester and an N-terminal cysteine lipid. This strategy mimics the natural glycosylphosphatidylinositol (GPI) linkage found in many natural membrane-associated proteins; however, the synthetic method utilizes simple lipid anchors without glycans. Synthetically lipidated recombinant green fluorescent protein (GFP) was shown to be stably anchored to the membrane, and its lateral fluidity was quantitatively characterized by direct fluorescence imaging in supported membranes. Circumventing the steps of purification from native cell membranes, this methodology facilitates the reconstitution of membrane-associated proteins.     

四丙基氢氧化铵改性纳米HZSM-5分子筛及其在甲醇制汽油中的催化性能

采用四丙基氢氧化铵(TPAOH)溶液对纳米ZSM-5分子筛进行改性, 运用X射线衍射、扫描电镜、²⁷Al和²⁹Si固体核磁、X射线光电子能谱、N₂物理吸附脱附法和NH₃程序升温脱附等手段对所制样品进行了表征, 并评价了其催化甲醇制汽油反应性能. 结果表明, 改性后的HZSM-5相对结晶度增加, 晶体形貌更加规整, 表面硅铝比增加, 比表面积和微孔表面积增大, 强酸位酸量增多. 同时, TPAOH改性不仅可以使分子筛脱硅脱铝, 而且伴有二次晶化补硅补铝, 改变了分子筛的硅铝分布. 改性的HZSM-5在甲醇制汽油反应中的稳定性大幅度提高, 其寿命由70h增至170h以上, 随着TPAOH处理时间的增加, 催化剂寿命增加, 氢转移反应加快, 导致油相产品中异构烷烃增多, 烯烃减少.     

Development of a PDEδ‐Targeting PROTACs that Impair Lipid Metabolism

The prenyl‐protein chaperone PDEδ modulates the localization of lipidated proteins in the cell, but current knowledge about its biological function is limited. Small‐molecule inhibitors that target the PDEδ prenyl‐binding site have proven invaluable in the analysis of biological processes mediated by PDEδ, like KRas cellular trafficking. However, allosteric inhibitor release from PDEδ by the Arl2/3 GTPases limits their application. We describe the development of new proteolysis‐targeting chimeras (PROTACs) that efficiently and selectively reduce PDEδ levels in cells through induced proteasomal degradation. Application of the PDEδ PROTACs increased sterol regulatory element binding protein (SREBP)‐mediated gene expression of enzymes involved in lipid metabolism, which was accompanied by elevated levels of cholesterol precursors. This finding for the first time demonstrates that PDEδ function plays a role in the regulation of enzymes of the mevalonate pathway.     

Semisynthesis of Functional Glycosylphosphatidylinositol‐Anchored Proteins

Glypiation is a common posttranslational modification of eukaryotic proteins involving the attachment of a glycosylphosphatidylinositol (GPI) glycolipid. GPIs contain a conserved phosphoglycan that is modified in a cell‐ and tissue‐specific manner. GPI complexity suggests roles in biological processes and effects on the attached protein, but the difficulties to get homogeneous material have hindered studies. We disclose a one‐pot intein‐mediated ligation (OPL) to obtain GPI‐anchored proteins. The strategy enables the glypiation of folded and denatured proteins with a natural linkage to the glycolipid. Using the strategy, glypiated eGFP, Thy1, and the Plasmodium berghei protein MSP1₁₉ were prepared. Glypiation did not alter the structure of eGFP and MSP1₁₉ proteins in solution, but it induced a strong pro‐inflammatory response in vitro. The strategy provides access to glypiated proteins to elucidate the activity of this modification and for use as vaccine candidates against parasitic infections.     

A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins

Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF₃)ppy)₂(dNMe₃bpy)]Cl₃, is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.     

Reversed approach to S-farnesylation and S-palmitoylation: application to an efficient synthesis of the C-terminus of lipidated human N-ras hexapeptide

[reaction: see text] A general reversed approach is described to synthesize S-palmitoylated and S-farnesylated peptides via S(N)2 displacement of bromide by reaction of a thiol group containing lipid as nucleophile with bromoalanine-containing peptides as electrophile. By employing this approach, lipidated peptides, including characteristic partial structures of human Ras peptides, were synthesized in good yields. This method gives access to farnesylated, palmitoylated, and doubly lipidated peptides.     

Semisynthesis of Functional Glycosylphosphatidylinositol-Anchored Proteins

Glypiation is a common posttranslational modification of eukaryotic proteins involving the attachment of a glycosylphosphatidylinositol (GPI) glycolipid. GPIs contain a conserved phosphoglycan that is modified in a cell- and tissue-specific manner. GPI complexity suggests roles in biological processes and effects on the attached protein, but the difficulties to get homogeneous material have hindered studies. We disclose a one-pot intein-mediated ligation (OPL) to obtain GPI-anchored proteins. The strategy enables the glypiation of folded and denatured proteins with a natural linkage to the glycolipid. Using the strategy, glypiated eGFP, Thy1, and the Plasmodium berghei protein MSP1₁₉ were prepared. Glypiation did not alter the structure of eGFP and MSP1₁₉ proteins in solution, but it induced a strong pro-inflammatory response in vitro. The strategy provides access to glypiated proteins to elucidate the activity of this modification and for use as vaccine candidates against parasitic infections.     

Development of a PDEδ-Targeting PROTACs that Impair Lipid Metabolism

The prenyl-protein chaperone PDEδ modulates the localization of lipidated proteins in the cell, but current knowledge about its biological function is limited. Small-molecule inhibitors that target the PDEδ prenyl-binding site have proven invaluable in the analysis of biological processes mediated by PDEδ, like KRas cellular trafficking. However, allosteric inhibitor release from PDEδ by the Arl2/3 GTPases limits their application. We describe the development of new proteolysis-targeting chimeras (PROTACs) that efficiently and selectively reduce PDEδ levels in cells through induced proteasomal degradation. Application of the PDEδ PROTACs increased sterol regulatory element binding protein (SREBP)-mediated gene expression of enzymes involved in lipid metabolism, which was accompanied by elevated levels of cholesterol precursors. This finding for the first time demonstrates that PDEδ function plays a role in the regulation of enzymes of the mevalonate pathway.     

Global Mapping of Protein–Lipid Interactions by Using Modified Choline-Containing Phospholipids Metabolically Synthesized in Live Cells

The protein–lipid interaction is an essential metabolic process that mediates cellular signaling and functions. Existing strategies for large-scale mapping studies of the protein–lipid interaction fall short in their incompatibility with metabolic incorporation or inability to remove unwanted interferences from lipidated proteins. By incorporating an alkyne-containing choline head group and a diazirine-modified fatty acid simultaneously into choline-containing phospholipids synthesized from live mammalian cells, protein–phospholipid interactions have been successfully imaged in live cells. Subsequent in situ profiling of the modified Cho phospholipid-crosslinked proteins followed by quantitative proteomics allowed identification of several hundred putative phospholipid-interacting proteins, some of which were further validated.     

Synthesis of functional Ras lipoproteins and fluorescent derivatives.

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.     

Intein-mediated synthesis of geranylgeranylated Rab7 protein in vitro

Production of recombinant proteins is an important prerequisite for biotechnology and life sciences in general. However, there is a paucity of methods for production of posttranslationally modified recombinant proteins or proteins with non-native functional groups, such as fluorophores, spin labels, and so forth. In this work we have used a combination of organic synthesis and in vitro protein ligation to construct monoprenylated Rab7 GTPase. The protein was prepared from a recombinant N-terminal portion and a peptide mimicking the C terminus of Rab7. For construction of a synthetic six-amino-acid-long fluorescent monoprenylated peptide, we used a block condensation strategy. Ligation was achieved with a yield of >70%. The resulting protein was purified from the unligated peptide by a combination of organic extraction and phase partitioning and refolding. The refolded monoprenylated semisynthetic Rab7 protein (Rab7GG) formed a stable complex with its natural chaperone REP-1 (Rab escort protein 1) and could serve as an acceptor of the second prenyl group in the enzymatic prenylation reaction. Using fluorescence spectroscopy, we characterized the interaction of the Rab7GG:REP-1 complex with Rab geranylgeranyl transferase and came to the conclusion that it functioned as a genuine intermediate of the prenylation reaction. Thus, we present the first example of the in vitro generation of a semisynthetic lipidated protein using the native chemical ligation method.     

Creating and Modulating Microdomains in Pore‐Spanning Membranes

The architecture of the plasma membrane is not only determined by the lipid and protein composition, but is also influenced by its attachment to the underlying cytoskeleton. Herein, we show that microscopic phase separation of “raft‐like” lipid mixtures in pore‐spanning bilayers is strongly determined by the underlying highly ordered porous substrate. In detail, lipid membranes composed of DOPC/sphingomyelin/cholesterol/Gb₃ were prepared on ordered pore arrays in silicon with pore diameters of 0.8, 1.2 and 2 μm, respectively, by spreading and fusion of giant unilamellar vesicles. The upper part of the silicon substrate was first coated with gold and then functionalized with a thiol‐bearing cholesterol derivative rendering the surface hydrophobic, which is prerequisite for membrane formation. Confocal laser scanning fluorescence microscopy was used to investigate the phase behavior of the obtained pore‐spanning membranes. Coexisting liquid‐ordered‐ (l_o) and liquid‐disordered (l_d) domains were visualized for DOPC/sphingomyelin/cholesterol/Gb₃ (40:35:20:5) membranes. The size of the l_o‐phase domains was strongly affected by the underlying pore size of the silicon substrate and could be controlled by temperature, and the cholesterol content in the membrane, which was modulated by the addition of methyl‐β‐cyclodextrin. Binding of Shiga toxin B‐pentamers to the Gb₃‐doped membranes increased the l_o‐phase considerably and even induced l_o‐phase domains in non‐phase separated bilayers composed of DOPC/sphingomyelin/cholesterol/Gb₃ (65:10:20:5).     

Transglutaminase-mediated synthesis of a DNA-(enzyme)n probe for highly sensitive DNA detection

A new synthetic strategy for DNA-enzyme conjugates with a novel architecture was explored using a natural cross-linking catalyst, microbial transglutaminase (MTG). A glutamine-donor substrate peptide of MTG was introduced at the 5-position on the pyrimidine of deoxyuridine triphosphate to prepare a DNA strand with multiple glutamine-donor sites by polymerase chain reaction (PCR). A substrate peptide that contained an MTG-reactive lysine residue was fused to the N terminus of a thermostable alkaline phoshatase from Pyrococcus furiosus (PfuAP) by genetic engineering. By combining enzymatically the substrate moieties of MTG introduced to the DNA template and the recombinant enzyme, a DNA-(enzyme)(n) conjugate with 1:n stoichiometry was successfully obtained. The enzyme/DNA ratio of the conjugate increased as the benzyloxycarbonyl-L-glutaminylglycine (Z-QG) moiety increased in the DNA template. The potential utility of the new conjugate decorated with signaling enzymes was validated in a dot blot hybridization assay. The DNA-(enzyme)(n) probe could clearly detect 10(4) copies of the target nucleic acid with the complementary sequence under harsh hybridization conditions, thereby enabling a simple detection procedure without cumbersome bound/free processes associated with a conventional hapten-antibody reaction-based DNA-detection system.     

Methanol to Gasoline over ZSM-5 Zeolite Treated with Alkaline Mixture with Different Ratios of TBA<Superscript>+</Superscript>/OH<Superscript>–</Superscript>

The influence of ZSM-5 (SiO₂/Al₂O₃ = 50) treatment with a tetrabutylamine hydroxide (TBAOH)/NaOH mixture having different mole ratios on its physicochemical properties and catalytic performance in the reaction of methanol to gasoline (MTG) was investigated. It was found that, with increasing ratio TBA⁺/OH^–, the crystallinities, micropore surface areas, micropore volumes, the amounts of strong acid sites and Brönsted acid sites gradually increased, and the mesopore volumes decreased. The treatment with pure TBAOH (TBA⁺/OH^– = 1.0) ensured the formation of narrow and uniform intracrystalline mesoporosity and the large amounts of strong or Brönsted acid sites on the zeolite, which contribute to the highest liquid hydrocarbon yield in the reaction of MTG.