Synthesis of functionalized rab GTPases by a combination of solution- or solid-phase lipopeptide synthesis with expressed protein ligation

Prenylated proteins with non-native functionalities are generally very difficult to obtain by recombinant or enzymatic means. The semisynthesis of preparative amounts of prenylated Rab guanosine triphosphatases (GTPases) from recombinant proteins and synthetic prenylated peptides depends largely on the availability of functionalised prenylated peptides corresponding to the proteins' native structure or modifications thereof. Here, we describe and compare solution-phase and solid-phase strategies for the generation of peptides corresponding to the prenylated C terminus of Rab7 GTPase. The solid-phase with utilisation of a hydrazide linker emerges as the more favourable approach. It allows a fast and practical synthesis of pure peptides and gives a high degree of flexibility in their modification. To facilitate the analysis of semisynthetic proteins, the synthesised peptides were equipped with a fluorescent group. Using the described approach, we introduced fluorophores at several different positions of the Rab7 C terminus. The position of the incorporated fluorescent groups in the peptides did not influence the protein-ligation reaction, as the generated peptides could be ligated onto thioester-tagged Rab7. However, it was found that the positioning of the fluorescent group had an influence on the functionality of the Rab7 proteins; analysis of the interaction of the semisynthetic Rab7 proteins with REP (Rab escort protein) and GDI (guanosine diphosphate dissociation inhibitor) molecules revealed that modification of the peptide side chains or of the C-terminal isoprenoid did not significantly interfere with complex formation. However, functionalisation of the C terminus was found to have an adverse effect on complex formation and stability, possibly reflecting low structural flexibility of the Rab GDI/REP molecules in the vicinity of the lipid-binding site.     

The analytical determination of isoprenoid intermediates from the mevalonate pathway

In this article, assays on the analytical determination of farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP), two important isoprenoid intermediates at biochemically relevant branching points in the mevalonate pathway, are summarized and reviewed. There is considerable recent interest in the measurement of these two isoprenoids because of their direct involvement in several diseases, for example, statins lower cholesterol by inhibiting 3-hydroxy-3-methylglutaryl-CoA reductase but equally affect other metabolite biosyntheses. The isoprenoids FPP and GGPP are key intermediates due to their role as CaaX-specific substrates for posttranslational modification of proteins (protein prenylation). Disease pathologies and therapeutic efficacy of different treatments (e.g., cholesterol-lowering drugs) may lead to a reduction in isoprenoid levels and an accompanying reduction in prenylation of specific proteins. To understand the exact biochemical role of the isoprenoids FPP and GGPP, we need to know their levels. Several recent studies have shown exact levels of FPP and GGP in plasma and relevant tissues and their modulation following treatment. Furthermore, by directly measuring the extent of protein prenylation and identifying target proteins, further insight into the exact biochemical nature of the pathology and regulatory mechanisms will be possible. This short review aims to highlight the relevant literature on the analytical determination of the free isoprenoids FPP and GGPP in biological tissue as well as techniques for directly measuring prenylated proteins.     

Diazotrifluoropropionamido-containing prenylcysteines: syntheses and applications for studying isoprenoid-protein interactions

Photoaffinity-labeled prenylcysteines (1 and 2) incorporating a diazotrifluoropropionamide-based photophore have been prepared. Photolyses of 2 in the presence of RhoGDI, a protein that interacts with prenylated proteins, and prenylcysteine-containing competitors demonstrate the effectiveness of this photoaffinity-labeled analogue as a tool for studying isoprenoid binding sites.     

Synthesis of fluorescently labeled mono- and diprenylated Rab7 GTPase

Modification of proteins with isoprenoid lipids is a widespread phenomenon in eukaryotic organisms that has received much attention due to its involvement in the progression of several diseases including cancer. Progress in studies of prenylated proteins has been hampered by difficulties associated with isolation of these proteins from native or recombinant sources. Small GTPases of the Rab family represent a particularly difficult example since they are doubly C-terminally geranylgeranylated and in some cases methylated. Here, we report an efficient and versatile strategy for the synthesis of mono- and digeranylgeranylated fluorescent RabGTPases using a combination of chemical synthesis and expressed protein ligation. Using this approach we generated fluorescent mono- and diprenylated Rab7 proteins that display near-native properties and form stoichiometric complexes with their natural chaperone REP-1. We demonstrate that the complex formed from semisynthetic monoprenylated Rab7 and REP-1 represents a genuine intermediate of the Rab prenylation reaction and thus provides a unique tool for studies of the Rab prenylation mechanism. Semisynthetic Rab7 proteins were used to develop a novel fluorescence-based in vitro prenylation assay. Using this assay we dissected the mechanism of the Rab7 double-geranylgeranylation reaction mediated by Rab geranylgeranyl transferase. We conclude that the reaction follows a random sequential mechanism. These results highlight the usefulness of the semisynthetic reaction intermediates in the study of protein posttranslational modification.     

Synthesis of farnesyl diphosphate analogues containing ether-linked photoactive benzophenones and their application in studies of protein prenyltransferases

Protein prenylation is a posttranslational lipid modification in which C(15) and C(20) isoprenoid units are linked to specific protein-derived cysteine residues through a thioether linkage. This process is catalyzed by a class of enzymes called prenyltransferases that are being intensively studied due to the finding that Ras protein is farnesylated coupled with the observation that mutant forms of Ras are implicated in a variety of human cancers. Inhibition of this posttranslational modification may serve as a possible cancer chemotherapy. Here, the syntheses of two new farnesyl diphosphate (FPP) analogues containing photoactive benzophenone groups are described. Each of these compounds was prepared in six steps from dimethylallyl alcohol. Substrate studies, inhibition kinetics, photoinactivation studies, and photolabeling experiments are also included; these experiments were performed with a number of protein prenyltransferases from different sources. A X-ray crystal structure of one of these analogues bound to rat farnesyltransferase illustrates that they are good substrate mimics. Of particular importance, these new analogues can be enzymatically incorporated into Ras-based peptide substrates allowing the preparation of molecules with photoactive isoprenoids that may serve as valuable probes for the study of prenylation function. Photoaffinity labeling of human protein geranylgeranyltransferase with (32)P-labeled forms of these analogues suggests that the C-10 locus of bound geranylgeranyl diphosphate (GGPP) is in close proximity to residues from the beta-subunit of this enzyme. These results clearly demonstrate the utility of these compounds as photoaffinity labeling analogues for the study of a variety of protein prenyltransferases and other enzymes that employ FPP or GGPP as their substrates.     

A rapid screening method for prenylated flavonoids with ultra‐high‐performance liquid chromatography/electrospray ionisation mass spectrometry in licorice root extracts

Due to their substitution with an isoprenoid group, prenylated flavonoids have an increased affinity for biological membranes and target proteins, enhancing their potential bioactivity. Although many prenylated flavonoids have been described, there are no methods that specifically screen for their presence in complex mixtures, prior to purification. We describe a method based on ultra‐high‐performance liquid chromatography (UHPLC) with electrospray ionisation mass spectrometry (ESI‐MS) that allows rapid screening for prenylated flavonoids in multi‐component plant extracts. Identification of the prenylated flavonoids is based on screening for neutral losses of 42 u and 56 u in the positive‐ion mode MS² and MS³ spectra within the MS chromatograms. In addition, this method discriminates between a prenyl chain and a ring‐closed prenyl (pyran ring), based on the ratio of the relative abundances of the ions that lose 42 u and 56 u (42:56). The application of this screening method on a 70% aq. ethanol, ethanol and ethyl acetate extract of the roots of Glycyrrhiza glabra indicated the presence of 70 mono‐ and di‐prenylated flavonoids. In addition, of each prenylated flavonoid the type of prenylation, chain or pyran ring was determined. Copyright © 2009 John Wiley & Sons, Ltd.     

A photoactive isoprenoid diphosphate analogue containing a stable phosphonate linkage: synthesis and biochemical studies with prenyltransferases

A number of biochemical processes rely on isoprenoids, including the post-translational modification of signaling proteins and the biosynthesis of a wide array of compounds. Photoactivatable analogues have been developed to study isoprenoid utilizing enzymes such as the isoprenoid synthases and prenyltransferases. While these initial analogues proved to be excellent structural analogues with good cross-linking capability, they lack the stability needed when the goals include isolation of cross-linked species, tryptic digestion, and subsequent peptide sequencing. Here, the synthesis of a benzophenone-based farnesyl diphosphate analogue containing a stable phosphonophosphate group is described. Inhibition kinetics, photolabeling experiments, as well as X-ray crystallographic analysis with a protein prenyltransferase are described, verifying this compound as a good isoprenoid mimetic. In addition, the utility of this new analogue was explored by using it to photoaffinity label crude protein extracts obtained from Hevea brasiliensis latex. Those experiments suggest that a small protein, rubber elongation factor, interacts directly with farnesyl diphosphate during rubber biosynthesis. These results indicate that this benzophenone-based isoprenoid analogue will be useful for identifying enzymes that utilize farnesyl diphosphate as a substrate.     

The isoprenoid-precursor dependence of Plasmodium spp

Due to the increase in resistance of Plasmodium spp. against available antimalarials, there is a need for new, effective and innovative drugs. The non-mevalonate pathway for the biosynthesis of the universal isoprenoid precursors, which is absent in humans, is suggested as an attractive source of targets for such drugs with a novel mode of action. The biological importance of this pathway to Plasmodium spp. is proven by the efficacy of the clinical candidate fosmidomycin, which inhibits the biosynthesis of isoprenoid precursors; it is, however, less clear which isoprenoid end products are essential for parasite survival. In this Highlight, we identify protein prenylation, isoprene-containing quinone production, N-linked glycosylation as well as carotenoid and vitamin-E biosynthesis as probably essential isoprenoid-dependent physiological processes in Plasmodium. Inhibition of any of these processes blocks parasite development. Furthermore, both protein prenylation of SNARE proteins and a protein tyrosine phosphatase as well as tRNA prenylation have been identified as isoprene-dependent processes for which the physiological role in Plasmodium remains unclear. Therefore, the biosynthetic route to the isoprenoid precursors presents attractive drug targets for the development of antimalarials with novel modes of action.     

Top-down analysis of protein isoprenylation by electrospray ionization hybrid quadrupole time-of-flight tandem mass spectrometry; the mouse Tgamma protein

Protein isoprenylation, an important post-translational modification with a lipid, involves the selective attachment of two types of isoprenoids, farnesyl (C15) and geranylgeranyl (C20). The isoprenoid is linked via a thioether bond to the C-terminal cysteine residue of a variety of cellular proteins, including the heterotrimeric G protein gamma-subunits. One member of the G protein family, transducin (Talpha/Tbetagamma), plays a central role in visual transduction, and the structure-function relationship has been extensively studied with purified proteins, predominantly with bovine transducin that was shown to be farnesylated at the C-terminal cysteine residue of the gamma-subunit (Tgamma). We report here the structure of the C-terminal modification of mouse Tgamma, which has not yet been elucidated owing to the low amount of protein that can be isolated from the mouse retina. Electrospray ionization mass spectrometry (ESI-MS) of the high-performance liquid chromatography (HPLC)-purified Tgamma was in good agreement with the calculated mass of the farnesylated and methylated form of mouse Tgamma (Pro1-Cys70). A 'top-down' analysis of intact Tgamma using an ESI hybrid quadrupole time-of-flight (TOF) tandem mass spectrometer provided isoprenyl-specific ions that were observed to produce ions separated by 204 Da from the conventional (unmodified) precursor ion or the C-terminal sequence ions. Such characteristic fragmentation on an isoprenoid observed in top-down analysis could be useful in general for determining the type of isoprenylation as well as probing the site of modification in the protein sequence.     

Benzophenone Photoprobes for Phosphoinositides, Peptides and Drugs

Benzophenones (BP) and related aryl ketone photophores have become established as the photoactivatable group of choice for high-efficiency covalent modification of hydrophobic regions of binding proteins, including enzymes and receptors that recognize peptide hormones, (oligonucleotides and nucleosides, phosphoinositides, inositol polyphosphates and a wide variety of therapeutic molecules. This review presents the advantages of BP as pho-toafnnity labels and provides specific examples from the last 3 years of applications of BP-containing ligands used in biochemistry.     

Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3

The cyanobacterial prenyltransferase AmbP3 catalyzes the reverse prenylation of the tetracyclic indole alkaloid hapalindole U at its C‐2 position. Interestingly, AmbP3 also accepts hapalindole A, a halogenated C‐10 epimer of hapalindole U, and catalyzes normal prenylation at its C‐2 position. The comparison of the two ternary crystal structures, AmbP3‐DMSPP/hapalindole U and AmbP3‐DMSPP/hapalindole A, at 1.65–2.00 Å resolution revealed two distinct orientations for the substrate binding that define reverse or normal prenylation. The tolerance of the enzyme for these altered orientations is attributed to the hydrophobicity of the substrate binding pocket and the plasticity of the amino acids surrounding the allyl group of the prenyl donor. This is the first study to provide the intimate structural basis for the normal and reverse prenylations catalyzed by a single enzyme, and it offers novel insight into the engineered biosynthesis of prenylated natural products.     

Photoaffinity analogues of farnesyl pyrophosphate transferable by protein farnesyl transferase

Farnesylation is a posttranslational lipid modification in which a 15-carbon farnesyl isoprenoid is linked via a thioether bond to specific cysteine residues of proteins in a reaction catalyzed by protein farnesyltransferase (FTase). We synthesized analogues (3-6) of farnesyl pyrophosphate (FPP) to probe the range of modifications possible to the FPP skeleton which allow for efficient transfer by FTase. Photoaffinity analogues of FPP (5, 6) were prepared by substituting perfluorophenyl azide functional groups for the omega-terminal isoprene of FPP. Substituted anilines replace the omega-terminal isoprene in analogues 3 and 4. Compounds 3-5 were prepared by reductive amination of the appropriate anilines with 8-oxo-geranyl acetate, followed by ester hydrolysis, chlorination, and pyrophosphorylation. Additional substitution of three methylenes for the beta-isoprene of FPP gave photoprobe 6 in nine steps. Preparation of the analogues required TiCl(4)-mediated imine formation prior to NaBH(OAc)(3) reduction for anilines with a pK(a) < 1. The azide moiety was not affected by Ph(3)PCl(2) conversion of allylic alcohols 13-16 into corresponding chlorides 17-20. Analogues 3-6 are efficiently transferred to target N-dansyl-GCVLS peptide substrate by mammalian FTase. Comparison of analogue structures and kinetics of transfer to those of FPP reveals that ring fluorination and para substituents have little effect on the affinity of the analogue pyrophosphate for FTase and its transfer efficiency. These results are also supported with models of the analogue binding modes in the active site of FTase. The transferable azide photoprobe 5 photoinactivates FTase. Transferable analogues 5 and 6 allow the formation of appropriately posttranslationally modified photoreactive peptide probes of isoprene function.     

Structure-function analysis of an enzymatic prenyl transfer reaction identifies a reaction chamber with modifiable specificity

Fungal indole prenyltransferases participate in a multitude of biosynthetic pathways. Their ability to prenylate diverse substrates has attracted interest for potential use in chemoenzymatic synthesis. The fungal indole prenyltransferase FtmPT1 catalyzes the prenylation of brevianamide F in the biosynthesis of fumitremorgin-type alkaloids, which show diverse pharmacological activities and are promising candidates for the development of antitumor agents. Here, we report crystal structures of unliganded Aspergillus fumigatus FtmPT1 as well as of a ternary complex of FtmPT1 bound to brevianamide F and an analogue of its isoprenoid substrate dimethylallyl diphosphate. FtmPT1 assumes a rare α/β-barrel fold, consisting of 10 circularly arranged β-strands surrounded by α-helices. Catalysis is performed in a hydrophobic reaction chamber at the center of the barrel. In combination with mutagenesis experiments, our analysis of the liganded and unliganded structures provides insight into the mechanism of catalysis and the determinants of regiospecificity. Sequence conservation of key features indicates that all fungal indole prenyltransferases possess similar active site architectures. However, while the dimethylallyl diphosphate binding site is strictly conserved in these enzymes, subtle changes in the reaction chamber likely allow for the accommodation of diverse aromatic substrates for prenylation. In support of this concept, we were able to redirect the regioselectivity of FtmPT1 by a single mutation of glycine 115 to threonine. This finding provides support for a potential use of fungal indole prenyltransferases as modifiable bioreactors that can be engineered to catalyze highly specific prenyl transfer reactions.     

催化NH吲哚的C2异戊烯基化反应:肽后期多样化和两步全合成tryprostatin B

异戊烯基化吲哚生物碱是一类同时具有吲哚环和类异戊二烯基团的天然产物,主要来源于各种真菌中.异戊烯基的存在可以增强化合物的亲脂性,使其能够更容易地穿过脂溶性的细胞膜与靶蛋白相结合,因此,这类天然产物往往表现出优异的生物活性.例如,从烟曲霉中分离的吲哚生物碱tryprostatins A和B是由L-色氨酸和L-脯氨酸组合而成,在吲哚骨架C2位连有异戊烯基,具有高效的抗肿瘤活性.在已知的全合成中,关键步骤C2位异戊烯基的引入,均是通过多步当量反应实现的.从原子和步骤经济性角度出发,发展高效催化方法实现NH吲哚C2位直接异戊烯基化反应具有重要的意义.但是由于吲哚的氮原子和C3位亲核性都较强,使得挑战很大.在生物体中,吲哚生物碱C2位异戊烯基的引入是通过酶催化实现的.二甲基烯丙基焦磷酸(DMAPP)先在酶作用下,生成异戊烯基碳正离子,然后与吲哚C2位进行傅克反应,引入异戊烯基.受这一生物过程启发,设想通过化学方法能够生成稳定的异戊烯基碳正离子,也可能实现吲哚C2异戊烯基化反应.本文采用廉价易得的1,1-二甲基烯丙醇为异戊烯基前体,对该想法进行了尝试.首先,以色醇为模板底物,对酸催化剂、溶剂及反应温度进行了筛选.在1,2-二氯乙烷(DCE)溶剂中,布朗斯特酸、路易斯酸和固体酸都能促进反应的进行,但会得到吲哚N和C2异戊烯基化两种产物,其中三氯化铝有较好的收率和选择性.通过对不同溶剂考察发现,2-甲基四氢呋喃是最佳溶剂,在80 oC下反应,目标产物收率为75％,产物选择性可达到12:1.随后,对不同类型的3-取代吲哚进行了普适性考察.对于色醇类底物,吲哚苯环上的取代基以及N上的保护基对反应影响不大,都能很顺利地参与反应.在标准条件下,色胺的异戊烯基化反应会发生在C3位,而以氯苯为溶剂时,可以提高C2位选择性,通过该方法可在抗衰老分子褪黑素(melatonin)的C2位引入异戊烯基.3-苯基和烷基取代的吲哚也是合适的底物.肽的后期修饰在生物医药中有着很重要的用途,因此,本文也将该异戊烯基化反应尝试用于修饰色氨酸类衍生物.保护的L-色氨酸酯以及色氨醇都能够顺利发生转化,以中等收率得到目标产物.L-色氨酸与其它各类氨基酸如甘氨酸、丙氨酸、亮氨酸、异亮氨酸、苯丙氨酸、甲硫氨酸、天冬氨酸等形成的肽也可进行C2异戊烯基化反应.此外,该转化过程中,可以完全保持手性,不会发生消旋化.特别是,L-色氨酸与L-脯氨酸酯形成的环二肽brevianamide F,在该条件下,也能发生C2位异戊烯基化反应,快速合成天然吲哚生物碱tryprostatin B.该反应有两种可能的路径,一种是吲哚C2位直接异戊烯基化,另一种是吲哚C3位先异戊烯基化,然后再重排到C2位.为进一步探索机理,对其进行了研究.首先,在标准条件下,3-酯基吲哚可以发生反应,C2位异戊烯基化产物收率为25％.然后,预先将异戊烯基引入C3位,合成了3-酯基-3-异戊烯基-3H吲哚,同样反应条件下,也能检测到目标产物,但收率只有5％.其次,以氘代1,1-二甲基烯丙醇为原料时,3-异戊烯基吲哚也能与其发生反应,并且在C3和C2位都观察到了氘代异戊烯基,两种产物比例为1:2,结果表明两种反应路径都是存在的,但吲哚C2位直接异戊烯基化是主要路径.此外,以固体酸Nafion为催化剂,离子液体[Bmim]Cl为反应介质,在120 oC时,3-取代吲哚与1,1-二甲基烯丙醇的反应选择性会发生改变,得到C2位异戊烯基异构化的产物.总之,以商业可得的1,1-二甲基烯丙醇为前体,首次实现了化学催化NH吲哚C2位直接异戊烯基化反应,获得较好的区域和化学选择性.该方法能够兼容各类官能团,底物适用性广,且可以用于褪黑素以及色氨酸衍生各种肽类化合物的后期修饰.基于该催化方法,可以两步全合成天然吲哚生物碱tryprostatin B,极大提高了合成效率,有助于实现放大生产.在固体酸/离子液体催化体系中,还实现了反应选择性的改变,丰富了产物类型.     

Analysis of the kinetic mechanism of recombinant human isoprenylcysteine carboxylmethyltransferase (Icmt)

Background  

Isoprenylcysteine carboxyl methyltransferase (Icmt) is the third of three enzymes that posttranslationally modify proteins that contain C-terminal CaaX motifs. The processing of CaaX proteins through this so-called prenylation pathway via a route initiated by addition of an isoprenoid lipid is required for both membrane targeting and function of the proteins. The involvement of many CaaX proteins such as Ras GTPases in oncogenesis and other aberrant proliferative disorders has led to the targeting of the enzymes involved in their processing for therapeutic development, necessitating a detailed understanding of the mechanisms of the enzymes.     

基于三甲基苯磺酰羟胺消除反应的氧连接氮乙酰葡萄糖胺修饰肽段的精准鉴定

氧连接氮乙酰葡萄糖胺(O-GlcNAc)是一种重要的蛋白质翻译后修饰,它在维持机体正常的生命活动中发挥着重要作用。许多研究证实,O-GlcNAc糖基化修饰稳态的破坏与人类多种疾病的发生相关,大规模富集鉴定O-GlcNAc糖基化修饰蛋白有助于发现新的临床疾病诊断标志物。由于O-GlcNAc糖基化修饰丰度较低,形成的糖苷键不稳定,O-GlcNAc糖基化修饰蛋白/肽段的富集鉴定面临一定挑战。近年来,全乙酰化的非天然糖代谢标记技术被广泛应用于O-GlcNAc糖基化修饰蛋白/肽段的富集鉴定。然而,最新的研究发现,在细胞代谢标记过程中,全乙酰化的非天然单糖会同时标记半胱氨酸的巯基而引入半胱氨酸巯基-叠氮糖人为修饰物。该副反应在一定程度上干扰了O-GlcNAc糖基化修饰蛋白/肽段的富集鉴定。鉴于此,研究发展了一种通过三甲基苯磺酰羟胺(MSH)特异性氧化消除半胱氨酸巯基-叠氮糖人为修饰物的方法,进而显著提高O-GlcNAc糖基化修饰肽段的精准鉴定。该方法建立于温和的磷酸钠缓冲液(50 mmol/L, pH=8)体系,利用过量的MSH,于95 ℃避光振荡反应30 min,可完全消除半胱氨酸巯基-叠氮糖人为修饰物。该方法应用于Hela细胞中,可有效消除叠氮全乙酰化半乳糖胺(Ac₄GalNAz)代谢产生的半胱氨酸巯基-叠氮糖人为修饰物,从而成功富集鉴定到157条O-GlcNAc糖基化修饰肽段,归属于130个蛋白质。该方法有效去除了半胱氨酸巯基-叠氮糖人为修饰物对代谢标记结果的干扰,为非天然糖代谢标记技术在糖蛋白组学分析中的应用提供了新的研究策略。     

One‐Pot N2C/C2C/N2N Ligation To Trap Weak Protein–Protein Interactions

Weak transient protein–protein interactions (PPIs) play an essential role in cellular dynamics. However, it is challenging to obtain weak protein complexes owing to their short lifetime. Herein we present a general and facile method for trapping weak PPIs in an unbiased manner using proximity‐induced ligations. To expand the chemical ligation spectrum, we developed novel N2N (N‐terminus to N‐terminus) and C2C (C‐terminus to C‐terminus) ligation approaches. By using N2C (N‐terminus to C‐terminus), N2N, and C2C ligations in one pot, the interacting proteins were linked. The weak Ypt1:GDI interaction drove C2C ligation with t_1/2 of 4.8 min and near quantitative conversion. The Ypt1‐GDI conjugate revealed that binding of Ypt1 G‐domain causes opening of the lipid‐binding site of GDI, which can accommodate one prenyl group, giving insights into Rab membrane recycling. Moreover, we used this strategy to trap the KRas homodimer, which plays an important role in Ras signaling.     

Synthesis and biological activity of photoactivatable N-ras peptides and proteins

A modular strategy for the assembly of farnesylated N-Ras heptapeptides carrying a photoactivatable benzophenone (BP) group within the lipid residue is described. This strategy is based on the fragment condensation of a N-terminal hexapeptide synthesized on the solid support with a cysteine methyl ester which is modified with different farnesyl analogues, incorporating the photophor. At the N-terminus of the peptides different functional groups can be attached, e.g., biotin for product enrichment and detection after photoactivation or a maleimido (MIC) linker, allowing for the coupling to proteins carrying a C-terminal free cysteine. Using this strategy, 24 peptides were synthesized, incorporating farnesyl analogues with four different chain lengths. Two of these photoactivatable conjugates were ligated to oncogenic human N-RasG12V Delta 181. A cellular transformation assay revealed that the semisynthetic proteins retain their biological activity despite the photolabel. The first photolabeling experiments with a geranyl-BP-labeled N-Ras construct and the farnesyl-sensitive guanine nucleotide exchange factor hSos1 indicate that this photoaffinity labeling system can be particularly useful for studying protein-protein interactions, e.g., the participation of the farnesyl group in Ras signaling, which is still discussed with controversy.     

Identification of prenylated pterocarpans and other isoflavonoids in Rhizopus spp. elicited soya bean seedlings by electrospray ionisation mass spectrometry

Phytoalexins from soya are mainly characterised as prenylated pterocarpans, the glyceollins. Extracts of non-soaked and soaked soya beans, as well as that of soya seedlings, grown in the presence of Rhizopus microsporus var. oryzae, were screened for the presence of prenylated flavonoids with a liquid chromatography/mass spectrometry (LC/MS)-based screening method. The glyceollins I-III and glyceollidins I-II, belonging to the isoflavonoid subclass of the pterocarpans, were tentatively assigned. The formation of these prenylated pterocarpans was accompanied by that of other prenylated isoflavonoids of the subclasses of the isoflavones and the coumestans. It was estimated that approx. 40% of the total isoflavonoid content in Rhizopus-challenged soya bean seedlings were prenylated pterocarpans, whereas 7% comprised prenylated isoflavones and prenylated coumestans. The site of prenylation (A-ring or B-ring) of the prenylated isoflavones was tentatively annotated using positive-ion mode MS by comparing the (1,3) A(+) retro-Diels-Alder (RDA) fragments of prenylated and non-prenylated isoflavones. Furthermore, the fragmentation pathways of the five pterocarpans in negative-ion (NI) mode were proposed, which involved the cleavage of the C-ring and/or D-ring. The absence of the ring-closed prenyl (pyran or furan) gave exclusively -H(2) O(x,y) RDA fragments, whereas its presence gave predominantly the common RDA fragments.     

Palladium in the Chemical Synthesis and Modification of Proteins

The field of site‐specific modification of proteins has drawn significant attention in recent years owing to its importance in various research areas such as the development of novel therapeutics and understanding the biochemical and cellular behaviors of proteins. The presence of a large number of reactive functional groups in the protein of interest and in the cellular environment renders modification at a specific site a highly challenging task. With the development of sophisticated chemical methodologies it is now possible to target a specific site of a protein with a desired modification, however, many challenges remain to be solved. In this context, transition metals in particular palladium‐mediated C−C bond‐forming and C−O bond‐cleavage reactions gained great interest owing to the unique catalytic properties of palladium. Palladium chemistry is being explored for protein modifications in vitro, on the cell surface, and within the cell. Very recently, palladium complexes have been applied for the rapid deprotection of several widely utilized cysteine protecting groups as well as in the removal of solubilizing tags to facilitate chemical protein synthesis. This Minireview highlights these advances and how the accumulated knowledge of palladium chemistry for small molecules is being impressively transferred to synthesis and modification of chemical proteins.