Installation of electrophiles onto the C-terminus of recombinant ubiquitin and ubiquitin-like proteins

Ubiquitin and related ubiquitin-like proteins (Ubls) influence a variety of cellular pathways including protein degradation and response to viral infections. The chemical interrogation of these complex enzymatic cascades relies on the use of tailored activity-based probes (ABPs). Herein, we report the preparation of ABPs for ubiquitin, NEDD8, SUMO2 and ISG15 by selective acyl hydrazide modification. Acyl hydrazides of Ubls are readily accessible by direct hydrazinolysis of Ubl-intein fusions. The suppressed pK_a and superior nucleophilicity of the acyl hydrazides enables their selective modification at acidic pH with carboxylic acid anhydrides. The modification proceeds rapidly and efficiently, and does not require chromatographic purification or refolding of the probes. We modified Ubl–NHNH₂ with various thiol-reactive electrophiles that couple selectively with E2s and DUBs. The ease of modification enables the rapid generation and screening of ubiquitin probes with various C-terminal truncations and warheads for the selection of the most suitable combination for a given E2 or DUB.

Preparation of acyl-hydrazide derived activity-based probes for ubiquitin-like proteins that show high reactivity and selectivity for deubiquitylases and E2 enzymes.     

Conjugation of proteins with chelating polymers via water-soluble carbodiimide andN-hydroxysulfosuccinimide

Water-soluble chelating polymers (CP) based on polylysine and diethylenetriaminepentaacetic acid (DTPA) have been prepared. The effect of the number of DTPA-groups in the polymer chain on the process of CP carbodiimide-mediated coupling to proteins has been studied. CP obtained were conjugated with proteins via carbodiimide andN-hydroxysulfosuccinimide (HSSI). The optimal conditions of CP activation were determined using model low-molecular-weight amine. It was shown that the addition of HSSI to an activation mixture increases the coupling efficiency of CP with immunoglobulins by 3‐4-fold compared with carbodiimide alone. Possible mechanisms of this phenomenon are discussed.     

Physiological functions of resistant proteins: proteins and peptides regulating large bowel fermentation of indigestible polysaccharide

Animal studies have shown conclusively that feeding of resistant starch (RS) increases production of large bowel total short-chain fatty acids (SCFAs). However, fermentation products of RS may be affected considerably by other dietary ingredients. In rats fed a 20% high-amylose cornstarch (HAS) with casein as the sole protein source, greater cecal SCFAs production was observed compared with that in rats fed a regular cornstarch diet. However, with this diet, the cecal succinate production was also very high. In contrast, when rice or potato protein with lower digestibility was used in place of casein, cecal succinate production decreased with a concomitant increase in butyrate. These observations suggest that nondigested protein, namely resistant protein, might play a role in correcting an imbalance in the ratio of carbohydrate and nitrogen as fermentative substrates for cecal bacteria and in promoting butyrate production. Epidemiological and biochemical data indicate a possible linkage between the fermentation products of starch (butyrate in particular) and the prevention of colorectal cancer as well as ulcerative colits. Accordingly, a fermentation strategy of RS favoring SCFA production should be established to elucidate the potentially beneficial effects of SCFAs on large bowel physiology.     

Conjugation reactions in the preparations of quantum dot-based immunoluminescent probes for analysis of proteins by capillary electrophoresis

A number of biologically important molecules, such as DNA, proteins, and antibodies, are routinely conjugated with fluorescent tags for high-sensitivity analyses. Here, the application of quantum dots in the place of bright and size-tunable luminophores is studied. Several selected bioconjugation reactions via zero-length cross-linkers, long-chain linkers, and oriented methods for linking of quantum dots with proteins were tested. Anti-ovalbumin, anti-proliferating cell nuclear antigen, anti-hemagglutinin, and anti-CD3 membrane protein as model antibodies and annexin V were used as high-specificity selectors. The reaction yield and efficiency of the prepared immunoluminescent probes were tested by capillary zone electrophoresis with laser-induced fluorescence detection.     

The kinetics of photochemical deconjugation reactions of methyl geranate

The photochemical transformations of methyl geranate are analyzed in terms of the dependence of quantum yield upon base, 1,2-dimethylimidazole, concentration. The dependence of quantum yield of deconjugated esters methyl (3Z)-3,7-dimethy1-3,6-octadienoate (12), methyl 3-methy1ene-7-methyl-6-octenoate (13) and methyl (3E)-3,7-dimethyl-3,6-octadienoate (14) and the ratio of (13)/(12) and (13)/(14) upon base concentration, as well as the dependence of the ratios (methyl 2-isopropenyl-5-methy1cyc1opentanecarboxy1ate (15): deconjugated ester) (10)/(12), (10)/(13) and (10)/(14) upon the reciprocal of the base concentration, are consistent with relative rate constant ratios for ([1,5] sigmatropic shift)/(dienol deprotonation) for photodienols 15, (precursor of 13), 17 (precursor of 12) and 19 (precursor of 14) of 72, 1.0 and 85.     

Affinity electrophoresis for studies of mechanisms regulating glycosylation of plasma proteins

A model system for studies of mechanisms governing the alterations of glycosylation of plasma glycoproteins was developed. The system employs two human hepatoma cell lines, Hep 3B and Hep G2, as target cells and agarose affinity electrophoresis with lectins for studies of microheterogeneity of alpha 1-protease inhibitor (PI), a model glycoprotein synthesized by hepatocytes. As an example for the application of the system, the effect of cytokines on major microheterogeneity of plasma proteins is demonstrated. The results indicate that interleukin 6, transforming growth factor beta 1 and, to some extent, tumor necrosis factor alpha are directly involved in regulating the pattern of glycosylation of plasma proteins in vitro, but the major effect is obtained by using combinations of interleukin 6, transforming growth factor beta 1, tumor necrosis factor alpha and interleukin 1. In addition, the results underline the dissociation between alteration of gene expression and the changes in the pattern of plasma protein glycosylation.     

Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants

A previous study, using capillary electrophoresis (CE) [J. Am. Chem. Soc. 2008, 130, 17384-17393], reported that six discrete complexes of ubiquitin (UBI) and sodium dodecyl sulfate (SDS) form at different concentrations of SDS along the pathway to unfolding of UBI in solutions of SDS. One complex (which formed between 0.8 and 1.8 mM SDS) consisted of native UBI associated with approximately 11 molecules of SDS. The current study used CE and (15)N/(13)C-(1)H heteronuclear single quantum coherence (HSQC) NMR spectroscopy to identify residues in folded UBI that associate specifically with SDS at 0.8-1.8 mM SDS, and to correlate these associations with established biophysical and structural properties of this well-characterized protein. The ability of the surface charge and hydrophobicity of folded UBI to affect the association with SDS (at concentrations below the CMC) was studied, using CE, by converting lys-ε-NH(3)(+) to lys-ε-NHCOCH(3) groups. According to CE, the acetylation of lysine residues inhibited the binding of 11 SDS ([SDS] < 2 mM) and decreased the number of complexes of composition UBI-(NHAc)(8)·SDS(n) that formed on the pathway of unfolding of UBI-(NHAc)(8) in SDS. A comparison of (15)N-(1)H HSQC spectra at 0 mM and 1 mM SDS with calculated electrostatic surface potentials of folded UBI (e.g., solutions to the nonlinear Poisson-Boltzmann (PB) equation) suggested, however, that SDS binds preferentially to native UBI at hydrophobic residues that are formally neutral (i.e., Leu and Ile), but that have positive electrostatic surface potential (as predicted from solutions to nonlinear PB equations); SDS did not uniformly interact with residues that have formal positive charge (e.g., Lys or Arg). Cationic functional groups, therefore, promote the binding of SDS to folded UBI because these groups exert long-range effects on the positive electrostatic surface potential (which extend beyond their own van der Waals radii, as predicted from PB theory), and not because cationic groups are necessarily the site of ionic interactions with sulfate groups. Moreover, SDS associated with residues in native UBI without regard to their location in α-helix or β-sheet structure (although residues in hydrogen-bonded loops did not bind SDS). No correlation was observed between the association of an amino acid with SDS and the solvent accessibility of the residue or its rate of amide H/D exchange. This study establishes a few (of perhaps several) factors that control the simultaneous molecular recognition of multiple anionic amphiphiles by a folded cytosolic protein.     

Chemistry and biology of the ubiquitin signal

Ubiquitination is one of the most utilized posttranslational modifications in eukaryotes and is involved in a wide range of cellular processes, but is mostly known as a signal for proteasomal degradation. Recently, it has become clear that the ubiquitin signal is far more complex and is dictated by the ubiquitin component and the substrate. The remarkable diversity of the ubiquitin signaling process has triggered an incredible amount of effort to investigate the role of ubiquitination on biological processes. However, despite more than three decades of studies, several important questions remain unanswered. A major hurdle is the inability to obtain homogeneous ubiquitin bioconjugates in sufficient amounts from cells or by application of the enzymatic machinery. Recent breakthroughs in chemical and semisynthetic strategies, however, offer solutions to these challenges. In this Review, we survey the fundamental biological aspects of the ubiquitin signal and present the emerging non-enzymatic approaches for overcoming these obstacles.     

Conjugation in the 1,2,3-triphenylbenzene system

The relative reactivity of 1,2,3-triphenylbenzene (20 with reference to benzene), and the partial rate factors for NO₂ substitution in positions 4,4′, and 4″ (18·6, 30, and 22·8 respectively) were determined by competitive nitration. The results suggest ‘conjugation effect’ as the factor responsible for the observed orientation and reactivity of the hydrocarbon in spite of its marked nonplanarity.     

聚合物蛋白质类药物单分子修饰的发展和展望

随着基因组学、生物化学、分子生物学及多肽合成等科学技术的发展,蛋白质及多肽药物已成为跨国医药企业竞相争夺未来生物医药领域的一个制高点。但是蛋白质类药物的临床应用受到了其理化及生物特性的种种限制,为了改善治疗效果,近年来聚合物修饰的蛋白质类药物有了长足的发展。本文着重回顾了蛋白质类药物聚乙二醇修饰的发展和现状,以及由此获得的优点和局限性;同时介绍了其它新型生物相容性聚合物蛋白质类药物修饰的最新研究进展,探讨了蛋白质类药物的"后聚乙二醇修饰"时代的可能方向和应用前景。     

Mapping the hydration dynamics of ubiquitin

The nature of water's interaction with biomolecules such as proteins has been difficult to examine in detail at atomic resolution. Solution NMR spectroscopy is potentially a powerful method for characterizing both the structural and temporal aspects of protein hydration but has been plagued by artifacts. Encapsulation of the protein of interest within the aqueous core of a reverse micelle particle results in a general slowing of water dynamics, significant reduction in hydrogen exchange chemistry and elimination of contributions from bulk water thereby enabling the use of nuclear Overhauser effects to quantify interactions between the protein surface and hydration water. Here we extend this approach to allow use of dipolar interactions between hydration water and hydrogens bonded to protein carbon atoms. By manipulating the molecular reorientation time of the reverse micelle particle through use of low viscosity liquid propane, the T(1ρ) relaxation time constants of (1)H bonded to (13)C were sufficiently lengthened to allow high quality rotating frame nuclear Overhauser effects to be obtained. These data supplement previous results obtained from dipolar interactions between the protein and hydrogens bonded to nitrogen and in aggregate cover the majority of the molecular surface of the protein. A wide range of hydration dynamics is observed. Clustering of hydration dynamics on the molecular surface is also seen. Regions of long-lived hydration water correspond with regions of the protein that participate in molecular recognition of binding partners suggesting that the contribution of the solvent entropy to the entropy of binding has been maximized through evolution.     

The alkoxide-catalyzed deconjugation of estra-4, 9-dien-3-ones

Chemistry of Natural Compounds -     

Conjugation of organic-metallic hybrid polymers and calf-thymus DNA

Strong electrostatic interaction between metallo-supramolecular polymers and DNA was confirmed by UV-vis and CD spectral measurements during titration, and cyclic voltammetry. The stable conjugation structure based on groove binding was revealed by using QM/MM computational methodology and supported by AFM.     

Formal synthesis of (+)-neooxazolomycin via a Stille cross-coupling/deconjugation route

A formal synthesis of neooxazolomycin is described via the preparation of Kende’s key intermediate in a longest linear sequence of 23 steps. This work is founded upon the union of three fragments: Moloney’s lactam-derived triflate, a vinyl stannane and a Julia-Kocienski sulfone and encompasses three key steps: (i) a Stille cross-coupling to combine the triflate and vinyl stannane, (ii) a base-promoted enone deconjugation to derive the dihydroxylation precursor and (iii) our previously reported Julia-Kocienski methodology to assemble the pentadienyl amine side chain with the sulfone precursor.     

Conjugation energy of some boron-containing systems

Summary The conjugation energies of some boron-containing heterocyclic compounds have been calculated. In a number of cases, in spite of the unusual valency angles, within the framework of the MO LCAO method in the -electron approximation, these systems prove to be stable.