‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS³ in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically ‘trigger’ the acquisition of an MS³ spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II.     

Adsorption of triton X-100 on silica gel: effects of temperature and alcohols

Adsorption of Triton X-100 (TX-100) on silica gel has been studied as a function of temperature (308–328 K) and composition for mixtures of water with ethanol or t-butanol. The adsorption capacity of silica gel for TX-100 decreases with increase in alcohol content. Adsorption isotherms of TX-100 on silica gel are four-region and were analyzed using the ARIAN (adsorption isotherm regional analysis) model. Data in regions 2, 3 and 4 were fitted to the Temkin, bilayer and reverse desorption isotherms, respectively. The results show that adsorption of TX-100 on silica gel in water and alcohol-water binary mixtures occurs mainly through formation of monolayer surface aggregates or low bilayer coverage.      

Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution

The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET.     

FPGA成为替代ASIC的最佳选择

多年来,Xilinx公司的可编程逻辑技术始终扮演着ASIC替代解决方案的角色.过去十多年来,每次当ASIC技术实现摩尔定律的预期,Xilinx FPGA和CPLD都迅速填补了由此而留下的间隙.最近,有些ASIC制造商推出了称为结构化ASIC(Structured ASIC)的改进ASIC结构,试图解决与基于标准单元的ASIC和门阵列相关的一些问题.但最终,人们都会问到这一决定性问题,"如果我们需要100万门至500万门的设计,到底哪种技术最佳地结合了硬件、软件和设计支持,从而可最好地满足我们的需要?"     

A facile synthesis of new 3-(2-benzimidazolyl)-2-alkyl-4-(3H)-quinazolinones under microwave irradiation

Preparation of 2-amino-N-(1-H-benzimidazol-2-yl)benzamide and a variety of new 3-(2-benzimidazolyl)-2-alkyl-4-(3H)-quinazolinones using isatoic anhydride, 2-aminobenzimidazole and orthoesters under microwave irradiation are described.     

Self‐Healing Polyester Urethane Supramolecular Elastomers Reinforced with Cellulose Nanocrystals for Biomedical Applications

Stretchable self‐healing urethane‐based biomaterials have always been crucial for biomedical applications; however, the strength is the main constraint of utilization of these healable materials. Here, a series of novel, healable, elastomeric, supramolecular polyester urethane nanocomposites of poly(1,8‐octanediol citrate) and hexamethylene diisocyanate reinforced with cellulose nanocrystals (CNCs) are introduced. Nanocomposites with various amounts of CNCs from 10 to 50 wt% are prepared using solvent casting technique followed by the evaluation of their microstructural features, mechanical properties, healability, and biocompatibility. The synthesized nanocomposites indicate significantly higher tensile modulus (approximately 36–500‐fold) in comparison to the supramolecular polymer alone. Upon exposure to heat, the materials can reheal, but nevertheless when the amount of CNC is greater than 10 wt%, the self‐healing ability of nanocomposites is deteriorated. These materials are capable of rebonding ruptured parts and fully restoring their mechanical properties. In vitro cytotoxicity test of the nanocomposites using human dermal fibroblasts confirms their good cytocompatibility. The optimized structure, self‐healing attributes, and noncytotoxicity make these nanocomposites highly promising for tissue engineering and other biomedical applications.     

Implementing and using high-order finite element methods

We present theoretical analyses of and detailed timings for two programs which use high-order finite element methods to solve the Navier- Strokes equations in two and three dimensions. The analyses show that algorithms popular in low-order finite element implementations are not always appropriate for high-order methods. The timings show that with the proper algorithms high-order finite element methods are viable for solving the Navier-Stokes equations. We show that it is more efficient, both in time and storage, not to precompute element matrices as the degree of approximating functions increases. We also study the cost of assembling the stiffness matrix versus directly evaluating bilinear forms in two and three dimensions. We show that it is more efficient not to assemble the full stiffness matrix for high-order methods in some cases. We consider the computational issues with regard to both Euclidean and isoparametric elements. We show that isoparametric elements may be used with higher-order elements without increasing the order of computational complexity.     

Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

An organocatalytic and highly regio‐, diastereo‐, and enantioselective intermolecular haloetherification and haloesterification reaction of allyl amides is reported. A variety of alkene substituents and substitution patterns are compatible with this chemistry. Notably, electronically unbiased alkene substrates exhibit exquisite regio‐ and diastereoselectivity for the title transformation. We also demonstrate that the same catalytic system can be used in both chlorination and bromination reactions of allyl amides with a variety of nucleophiles with little or no modification.     

Cyclopropanation and epoxidation of 2-ylidene derivatives of lupane series

Russian Journal of Organic Chemistry - Crotone condensation of allobetulone with fluorine-containing benzaldehydes afforded new α,β-unsaturated ketones of lupane series. Their...