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.     

Utilization of Nucleotide Probes in PCR‐ELISA Procedure for the Quantitative Determination of Plasmodium Falciparum DNA in Malaria

Abstract

The research work reported herein is the development of a simple and specific quantitative procedure for the determination of P. falciparum DNA in malaria that involves the direct detection of the highly 42‐kDa conserved C‐terminal regiopn of P. falciparum merozoite surface protein gene (MSP1 ₄₂ gene). This procedure entails the amplification of the MSP1 ₄₂ gene by using the PCR technique in the presence of digoxigenin‐11‐dUTP and the synthesis of the specific biotin label nucleotide probes directed to the MSP1 ₄₂ gene. These specific probes are then used in the Enzyme Linked Immunosorbent Assay (ELISA) for the quantitative determination of the MSP1 ₄₂ gene which leads to the quantitative determination of P. falciparum DNA in malaria for quantitative diagnostic purpose. The P. falciparum malaria diagnostic results obtained from a small number of 18 whole blood samples show that the present quantitative PCR‐ELISA procedure allows the quantitative determination of P. falciparum DNA in malaria with a sensitivity and specificity over to those of the current standard microscopic examination. This quantitative PCR‐ELISA procedure is not only important for quantitative P. falciparum malaria diagnosis but also useful for monitoring the efficacy of any existing anti‐malarial drug as well as for testing the efficacy of any malaria vaccine.     

Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification

Fluorobenzene probes for protein profiling through selective cysteine labeling have been developed by rational reactivity tuning. Tuning was achieved by selecting an electron‐withdrawing para substituent in combination with variation of the number of fluorine substituents. Optimized probes chemoselectively arylated cysteine residues in proteins under aqueous conditions. Probes linked to azide, biotin, or a fluorophore were applicable to labeling of eGFP and albumin. Selective inhibition of cysteine proteases was also demonstrated with the probes. Additionally, probes were tuned for site‐selective labeling of cysteine residues and for activity‐based protein profiling in cell lysates.     

Modification of β2 I by glutardialdehydeI by glutardialdehyde

Autoantibodies from patients with antiphospholipid syndrome (APS) recognize an epitope on β₂glycoprotein I (β₂GPI) only when native β₂GPI is adsorbed on surfaces composed of anionic phospholipids or oxidized polystyrene, β₂GPI was modified with the crosslinking agent, glutardialdehyde (GDA), which induced exposure of the anti-β₂GPI epitope at GDA: β₂GPI mol ratios in the range of 500–2000. A second crosslinking agent, dimethyl-suberimidate (DMS), did not expose the epitope, which may be a consequence of its having less tendency than GDA to form intermolecular links. SDS-PAGE experiments demonstrate that GDA does promote extensive intermolecular crosslinking of β₂GPI, and DMS does not. Formaldehyde also reacts with the lysine residues of β₂GPI, but does not expose the epitope. The circular dichroism spectra of native and modified β₂GPI confirm that GDA induces changes in conformation that are qualitatively different from those caused by formaldehyde. These data provide evidence that binding of lysine residues is not a sufficient condition for exposure of the autoepitope, and also support the likelihood that β₂GPI antibodies bind only to aggregates of the protein. Thus, by synthesizing an active holoantigen of β₂GPI, conditions were defined that are necessary for binding of human autoantibodies. The authors also suggest that treatment of phospholipid-binding proteins with chemical agents might provide a strategy to modify their structure and permit exposure of epitopes, resulting in synthetic antigens for therapeutic and diagnostic use.     

Fast and Stable N‐Terminal Cysteine Modification through Thiazolidino Boronate Mediated Acyl Transfer

We report a novel conjugation of N‐terminal cysteines (NCys) that proceeds with fast kinetics and exquisite selectivity, thereby enabling facile modification of NCys‐bearing proteins in complex biological milieu. This new NCys conjugation proceeds via a thiazolidine boronate (TzB) intermediate that results from fast (k₂: ≈5000 m ^?1 s^?1) and reversible conjugation of NCys with 2‐formylphenylboronic acid (FPBA). We designed a FPBA derivative that upon TzB formation elicits intramolecular acyl transfer to give N‐acyl thiazolidines. In contrast to the quick hydrolysis of TzB, the N‐acylated thiazolidines exhibit robust stability under physiologic conditions. The utility of the TzB‐mediated NCys conjugation is demonstrated by rapid and non‐disruptive labeling of two enzymes. Furthermore, applying this chemistry to bacteriophage allows facile chemical modification of phage libraries, which greatly expands the chemical space amenable to phage display.     

Universal Approach Towards r‐Hirudin Derivatives with High Anti‐Thrombin Activity Based on Chemical Differentiation of Primary Amino Groups

Chemical modification of recombinant hirudin (r‐hirudin) is necessary whenever surface‐confinement to a biomaterial or biotinylation for subsequent conjugation with carriers is intended. Here, we report a modification strategy that permits chemical discrimination between r‐hirudin's amino groups and preserves its thrombin inhibitor activity. By reaction with Msc‐ONSu, protective groups were successively introduced in r‐hirudin yielding four derivatives (Msc)_x‐hirudin (1 ≤ x ≤ 4) and pure fractions were isolated by ion exchange chromatography. Structure–function relationships were studied for all derivatives and revealed a decrease in activity of more than 90% as compared to unprotected r‐hirudin. MALDI‐TOF MS was used to determine the locations of the Msc groups. Furthermore, evidence was provided that r‐hirudin's N‐terminal amino group is highly important for its anti‐thrombin activity. Selective modification of the lysine residues which maintained the free N‐terminal amino group preserved the anti‐thrombin activity of r‐hirudin even after biotinylation and subsequent linkage to streptavidin or confinement to a polymer surface.     

Inositolphosphoglycan Mediators: An Effective Synthesis of the Conserved Linear GPI Anchor Structure*

An effective new preparative synthesis of the conserved linear pseudopentasaccharide structure of the GPI anchors and of the full GPI structure has been carried out that has permitted obtaining both molecules in sufficient quantities as to perform further structural and biologic studies. The synthesis involves a 3+2 block synthesis strategy in which a conveniently protected Man α(1→4) GlcN₃ α(1→6) myo‐Ins building block, previously used in the synthesis of inositolphosphoglycan (IPG) mediators, is glycosylated with a protected Man α(1→2) Man trichloroacetimidate.     

Accessible Mannitol‐Based Amphiphiles (MNAs) for Membrane Protein Solubilisation and Stabilisation

Integral membrane proteins are amphipathic molecules crucial for all cellular life. The structural study of these macromolecules starts with protein extraction from the native membranes, followed by purification and crystallisation. Detergents are essential tools for these processes, but detergent‐solubilised membrane proteins often denature and aggregate, resulting in loss of both structure and function. In this study, a novel class of agents, designated mannitol‐based amphiphiles (MNAs), were prepared and characterised for their ability to solubilise and stabilise membrane proteins. Some of MNAs conferred enhanced stability to four membrane proteins including a G protein‐coupled receptor (GPCR), the β₂ adrenergic receptor (β₂AR), compared to both n‐dodecyl‐d ‐maltoside (DDM) and the other MNAs. These agents were also better than DDM for electron microscopy analysis of the β₂AR. The ease of preparation together with the enhanced membrane protein stabilisation efficacy demonstrates the value of these agents for future membrane protein research.     

Defining topological features of membrane proteins by nanoelectrospray ionisation mass spectrometry

The D‐galactose‐H⁺ symport protein, GalP, of Escherichia coli is the bacterial homologue of the human glucose transport protein, GLUT1. Here we demonstrate that mass spectrometry can be used to map modification by covalently bound reagents, and also to detect structural changes in the GalP protein that occur upon substrate binding. The small thiol‐group‐specific reagent N‐ethylmaleimide (NEM) was used to modify the cysteine residues in GalP(His)₆ both alone and in the presence of D‐glucose, a known substrate. Employing a mixture of proteolysis and thermal degradation methods, the three cysteine residues were found to undergo sequential reactions with NEM, with Cys374 being modified first, followed by Cys389 and finally Cys19, thus indicating their different accessibilities within the three‐dimensional structure of the protein. Prior binding of the substrate D‐glucose to the protein protected Cys19 and Cys374 against NEM modification, but not Cys389. Cys374 had been expected to be shielded by D‐glucose binding while Cys389 had been expected to be unaffected, consistent with their proposed respective locations in the vicinity of, and distant from, the sugar binding site. However, the inaccessibility of Cys19 was unexpected and suggests a structural change in the protein promoted by D‐glucose binding which changes the proximity of Cys19 with respect to the D‐glucose‐binding site. Copyright © 2010 John Wiley & Sons, Ltd.     

Chemical Biology of Glycosylphosphatidylinositol Anchors

Glycosylphosphatidylinositols (GPIs) are complex glycolipids that are covalently linked to the C‐terminus of proteins as a posttranslational modification. They anchor the attached protein to the cell membrane and are essential for normal functioning of eukaryotic cells. GPI‐anchored proteins are structurally and functionally diverse. Many GPIs have been structurally characterized but comprehension of their biological functions, beyond the simple physical anchoring, remains largely speculative. Work on functional elucidation at a molecular level is still limited. This Review focuses on the roles of GPI unraveled by using synthetic molecules and summarizes the structural diversity of GPIs, as well as their biological and chemical syntheses.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data

Functional motions of ¹⁵N‐labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R_1ρ and CPMG‐type experiments. CEST also simultaneously reports on site‐specific R₁ and R₂ parameters. It is shown here how CEST‐derived R₁ and R₂ relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a “lean” version of the model‐free approach S² order parameters can be determined that match those from the standard model‐free approach applied to ¹⁵N R₁, R₂, and {¹H}‐¹⁵N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond‐to‐millisecond timescales.     

Phosphonylation Controls the Protein Corona of Multifunctional Polyglycerol‐Modified Nanocarriers

Nanocarriers are a platform for modern drug delivery. In contact with blood, proteins adsorb to nanocarriers, altering their behavior in vivo. To reduce unspecific protein adsorption and unspecific cellular uptake, nanocarriers are modified with hydrophilic polymers like poly(ethylene glycol) (PEG). However, with PEG the attachment of further functional structures such as targeting units is limited. A method to introduce multifunctionality via polyglycerol (PG) while maintaining the hydrophilicity of PEG is introduced. Different amounts of negatively charged phosphonate groups (up to 29 mol%) are attached to the multifunctional PGs (M_n 2–4 kg mol^?1, Ð < 1.36) by post‐modification. PGs are used in the miniemulsion/solvent evaporation procedure to prepare model nanocarriers. Their behavior in human blood plasma is investigated to determine the influence of the negative charges on the protein adsorption. The protein corona of PGylated nanocarriers is similar to PEGylated analogs (on same nanocarriers), but the protein pattern could be gradually altered by the integration of phosphonates. This is the first report on the gradual increase of negative charges on nanocarriers and intriguingly up to a certain amount of phosphonate groups per nanocarrier the protein pattern remains relatively unchanged, which is important for the future design of nanocarriers.     

Reactivity-based One-pot Synthesis of Immunosuppressive Glycolipids from the Caribbean Sponge Plakortis simplex

The first synthesis of three natural glycolipid simplexides 1a – 1c , which were isolated from the marine sponge Plakortis simplex and claimed to inhibit T cell proliferation, has been concisely accomplished by a reactivity‐based one‐pot synthetic strategy under the use of p‐toluenethioglycoside (STol) donors.     

A Stable Isotopic Pre-digestion Labeling Method for Protein Quantitative Analysis Using Matrix-assisted Laser Desorption/ionization Mass Spectrometry

As an extension of our previous work, here a strategy was demonstrated for protein identification and quantification analyses utilizing a combination of stable isotope chemical labeling with subsequent denaturation, enzymatic digestion and matrix assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Using [d₀]‐ and [d₆]‐4,6‐dimethoxy‐2‐(methylsulfonyl)pyrimidine ([d₀]‐/[d₆]‐DMMSP), stable isotopic labels were incorporated before digestion. The comparative samples were combined before labeling after digestion, thus biases resulting from differences in sample digestion were avoided and the higher accuracy of quantification could be attained. The labeling was spatial‐selective to particular residues of cysteine, lysine, and tyrosine before denaturation, which could lead to a better universality of the strategy for cysteine‐free proteins. In addition, some lysine residues were blocked after labeling, the partly destroyed recognition sites could simplify the trypsin hydrolysates and hence facilitate the MS complexity. Together, our one‐step labeling strategy combined several desirable properties such as spatial‐selective labeling, reliability of quantitative results, simplification of analysis of complex systems and direct analysis with minimum sample handling. Our results demonstrate the usefulness of the method for analyzing lysozyme in egg white. The method was expected to provide a new powerful tool for comparative proteome research.     

DNA-Mediated Stack Formation of Nanodiscs

Membrane-scaffolding proteins (MSPs) derived from apolipoprotein A-1 have become a versatile tool in generating nano-sized discoidal membrane mimetics (nanodiscs) for membrane protein research. Recent efforts have aimed at exploiting their controlled lipid protein ratio and size distribution to arrange membrane proteins in regular supramolecular structures for diffraction studies. Thereby, direct membrane protein crystallization, which has remained the limiting factor in structure determination of membrane proteins, would be circumvented. We describe here the formation of multimers of membrane-scaffolding protein MSP1D1-bounded nanodiscs using the thiol reactivity of engineered cysteines. The mutated positions N42 and K163 in MSP1D1 were chosen to support chemical modification as evidenced by fluorescent labeling with pyrene. Minimal interference with the nanodisc formation and structure was demonstrated by circular dichroism spectroscopy, differential light scattering and size exclusion chromatography. The direct disulphide bond formation of nanodiscs formed by the MSP1D1_N42C variant led to dimers and trimers with low yield. In contrast, transmission electron microscopy revealed that the attachment of oligonucleotides to the engineered cysteines of MSP1D1 allowed the growth of submicron-sized tracts of stacked nanodiscs through the hybridization of nanodisc populations carrying complementary strands and a flexible spacer.     

Sugar–Protein Connectivity Impacts on the Immunogenicity of Site‐Selective Salmonella O‐Antigen Glycoconjugate Vaccines

A series of glycoconjugates with defined connectivity were synthesized to investigate the impact of coupling Salmonella typhimurium O‐antigen to different amino acids of CRM₁₉₇ protein carrier. In particular, two novel methods for site‐selective glycan conjugation were developed to obtain conjugates with single attachment site on the protein, based on chemical modification of a disulfide bond and pH‐controlled transglutaminase‐catalyzed modification of lysine, respectively. Importantly, conjugation at the C186‐201 bond resulted in significantly higher anti O‐antigen bactericidal antibody titers than coupling to K37/39, and in comparable titers to conjugates bearing a larger number of saccharides. This study demonstrates that the conjugation site plays a role in determining the immunogenicity in mice and one single attachment point may be sufficient to induce high levels of bactericidal antibodies.     

Hydroxamic Acid‐Piperidine Conjugate is an Activated Catalyst for Lysine Acetylation under Physiological Conditions

Lysine acylation of proteins is an essential chemical reaction for posttranslational modification and as a means of protein modification in various applications. N,N‐Dimethyl‐4‐aminopyridine (DMAP) derivatives are widely‐used catalysts for lysine acylation of proteins; however, the DMAP moiety mostly exists in a protonated, and thus deactivated, form under physiological conditions due to its basicity. An alternative catalytic motif furnishing higher acylation activity would further broaden the possible applications of chemical lysine acylation. We herein report that the hydroxamic acid‐piperidine conjugate Ph‐HXA is a more active catalytic motif for lysine acetylation than DMAP under physiological conditions. In contrast to DMAP, the hydroxamic acid moiety is mostly deprotonated under aqueous neutral pH, resulting in a higher concentration of the activated form. The Ph‐HXA catalyst is also more tolerant of deactivation by a high concentration of glutathione than DMAP. Therefore, Ph‐HXA might be a suitable catalytic motif for target protein‐selective and site‐selective acetylation in cells.     

Fast and Tight Boronate Formation for Click Bioorthogonal Conjugation

A new click bioorthogonal reaction system was devised to enable the fast ligation (k_ON≈340 m ^?1 s^?1) of conjugatable derivatives of a rigid cyclic diol (nopoldiol) and a carefully optimized boronic acid partner, 2‐methyl‐5‐carboxymethylphenylboronic acid. Using NMR and fluorescence spectroscopy studies, the corresponding boronates were found to form reversibly within minutes at low micromolar concentration in water, providing submicromolar equilibrium constant (K_eq≈10⁵–10⁶ m ^?1). Efficient protein conjugation under physiological conditions was demonstrated with model proteins thioredoxin and albumin, and characterized by mass spectrometry and gel electrophoresis.     

Characterization of green‐tissue protein extract from alfalfa (Medicago sativa) exploiting a 3‐D technique

There is a growing interest of pharmaceutical companies for plant‐based production systems. To facilitate the general acceptance of plants as bioreactors, the establishment of efficient downstream operations is critical. It has been proposed that a better understanding of the properties of the contaminant proteins can benefit downstream processing design and operation. The coupled application of 2‐DE with aqueous two‐phase partitioning has been suggested as a practical 3‐D method to characterize potential contaminant proteins from plant extracts. The application of this novel 3‐D approach to a complex protein extract from alfalfa (Medicago sativa) containing a model recombinant protein (human granulocyte colony stimulating factor (hG‐CSF)) resulted in the quantification of 55 protein spots. The 3‐D properties (M_r, pI, and K_p) obtained for 17 proteins comprising 69% of the alfalfa proteins, allowed the proposal of a prefractionation step as well as the identification of the target molecule (rG‐CSF) from bulk of alfalfa proteins. The information obtained from this experimental approach was useful for the identification of the potential contaminant proteins that will occur in alfalfa when this plant is used as a host for recombinant proteins. Additionally, this method will assist in the design of adequate purification strategies for recombinant proteins expressed in alfalfa green tissue.