A top-down approach to protein structure studies using chemical cross-linking and Fourier transform mass spectrometry

In a preliminary communication we described a top-down approach to the determination of chemical cross-link location in proteins using Fourier transform mass spectrometry (FT-MS). We have since extended the approach to use a series of homobifunctional cross-linkers with the same reactive functional groups, but different cross-linker arm lengths. Correlating cross-linking data across a series of related linkers allows the distance constraint derived from a cross-link between two reactive side chains to be determined more accurately and increases the confidence in the assignment of the cross-links. In ubiquitin, there are seven lysines with primary amino groups and the amino terminus. Disuccinimidyl suberate (DSS, cross-linker arm length = 11.4 A), disuccinimidyl glutarate (DSG, cross-linker arm length = 7.5 A) and disuccinimidyl tartrate (DST, cross- linker arm length = 5.8 A) are homobifunctional cross-linking reagents that react specifically with primary amines. Using tandem mass spectrometry (MS/MS) on the singly, internally cross-linked precursor ion of ubiquitin, we found cross-links with DSS and DSG between the amino terminus and Lys 6, between Lys 6 and Lys 11, and between Lys 63 and Lys 48. Using disuccinimidyl tartrate (DST), the shortest cross-linker in the series, only the cross-links between the amino terminus and Lys 6, and between Lys 6 and Lys 11 were observed. The observed cross-links are consistent with the crystal structure of ubiquitin, if the lysine side chains and the amino terminus are assumed to have considerable flexibility. In a separate study, we probed the reactivity of the primary amino groups in ubiquitin using the amino acetylating reagent, N-hydroxy succinimidyl acetate (NHSAc), and a top-down approach to localize the acetylated lysine residues. The reactivity order obtained in that study (M1 approximate, equals K6 approximate, equals K48 approximate, equals K63) > K33 > K11 > (K27, K29), shows that the cross-link first formed in ubiquitin by reaction with DSS and DSG occurs between the most reactive residues.     

Densitometric Determination of Embelin in Lysimachia punctata

JPC – Journal of Planar Chromatography – Modern TLC - Athin layer chromatographic method with densitometric UV detection at λ = 285 nm has been developed for quantification of...     

Bis­(melaminium) dl‐malate tetrahydrate

The crystal structure of the title melaminium salt, bis(2,4,6‐tri­amino‐1,3,5‐triazin‐1‐ium) dl ‐malate tetrahydrate, 2C₃H₇N₆⁺·C₄H₄O₅²⁻·4H₂O, consists of singly protonated melaminium residues, dl ‐malate dianions and water mol­ecules. The melaminium residues are connected into chains by four N—H⃛N hydrogen bonds, and these chains form a stacking structure along the c axis. The dl ‐malate dianions form hydrogen‐bonded chains and, together with hydrogen‐bonded water mol­ecules, form a layer parallel to the (100) plane. The conformation of the malate ion is compared with an ab initio molecular‐orbital calculation. The oppositely charged moieties, i.e. the stacks of melaminium chains and hydrogen‐bonded dl ‐malate anions and water mol­ecules, form a three‐dimensional polymeric structure, in which N—H⃛O hydrogen bonds stabilize the stacking.     

Multifunctional polyesters as new candidate materials for biomedical applications. Synthesis and structural characterization

The present work was aimed at the development of functional polymeric materials to be used in the targeted delivery of proteic drug and tissue engineering fields. The adopted strategy was based on the design of special polymer classes whose structures and functionality could be easily modified by finely tuned synthetic procedures. Poly(ether ester)s containing H-bonding units were chosen as promising materials for the proposed applications. Commercially available precursors were successfully used for the synthesis of symmetrical diesters containing different H-bonding groups (amide, carbamate, and urea moieties). In all cases, pure products were obtained in good yields. Bulk polycondensation of the monomeric precursors with different mixtures of 1,4-butanediol and PEG 1000 diol afforded a variety of high molecular weight polymeric structures. Physical-chemical characterization of the polymers indicates that their thermal, mechanical, and swelling properties can be tailored by a proper selection of the H-bonding group and of the composition of the feed mixture.     

Studies of the reactions between indole-2,3-diones (isatins) and 2-aminobenzylamine

Reflux of equimolecular amounts 2-aminobenzylamine and isatins in acetic acid produced indolo[3,2-c]quinolin-6-ones in good yields. A proposed mechanism involving initial formation of a spiro compound is given. This isolable intermediate subsequently rearranges via a sequential isocyanate ring opening and a cyclisation process to a urea derivative which finally cyclized to the indolo[3,2-c]quinolin-6-ones. The urea derivative could be prepared separately and cyclized selectively to indolo[3,2-c]quinolin-6-one. Reaction of N-acetylisatin with 2-aminobenzylamine at room temperature yielded the 1,4-benzodiazepinone 3-(2-acetamidophenyl)-1,5-dihydro-1,4-benzodiazepin-2-one whereas its isomer 2(2-acetamidophenyl)-4,5-dihydro-1,4-benzodiazepin-3-one was obtained from 2-(2-acetylaminophenyl)-N-(2-aminobenzyl)-2-oxoacetamide in acetic acid at room temperature.The previously unknown linear isomer of indolo[3,2-c]quinolin-6-one, i.e. indolo[2,3-b]quinolin-11-one, has been prepared by thermal (260°C) cyclization of methyl 2-phenylamino indole-3-carboxylate, which in turn was prepared in two steps from methyl indole-3-carboxylate.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.     

Zirconium-mediated conversion of homoallylic ethers into cyclopropane derivatives

Homoallylic ethers react with Cp₂ZrCl₂/2 n-BuLi reagent to afford cyclopropane derivatives. Cyclopropylcarbinyl-homoallyl rearrangements involving zirconium species are observed depending on the substrate structure.     

A new insight into the understanding of the collapsed form of poly(N-isopropylacrylamide) molecules

Possible collapsed forms of poly(N-isopropylacrylamide) molecules are reviewed on the basis of first principle calculations. Various configurations and associated conformations are detailed. The calculated optimized structures exhibit different possibilities of creating networks of intra-molecular bonds of the hydrogen type. We show that the most remarkable one is able to form a local, self-saturated and well ordered helix. We also indicate in which direction the synthesis of the molecule should be oriented to improve its global behavior in term of hydrophobic/hydrophilic behavior.