Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

Synthesis and structure of tetraphenylantimony hydrogen phthalate

Tetraphenylantimony hydrogen phthalate, Ph4SbOC(O)C6H4000H-o, was prepared by the reaction of pentaphenylantimony with phthalic acid. According to the data of X-ray structural analysis, the resulting compound is a trigonal-bipyramidal complex of antimony with three phenyl groups in equatorial positions; the fourth phenyl group and the carboxyl fragment are in axial positions. The CSbO angle is 177.5(1)° the Sb-C(Ph)_eq and Sb-C(Ph)ax distances are 2.099(4)-2.177(4) A and 2.129(4) A, respectively. The H atom of the free carboxyl group and the carbonyl O atom of another carboxylate group form an intramolecular hydrogen bond.DeceasedTranslated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 2082–2085, August, 1996.     

Properties and structures of porphyrexides

The molecular and crystal structures of porphyrexides, viz., 4-amino-2-imino-(1) and (Z)-2-amino-4-bromoimino-5,5-dimethyl-4,5-dihydro-1H-imidazole 1-oxyls (7), and their diamagnetic precursors were determined. Compound 1 is kinetically unstable because it is oxidized with atmospheric oxygen to form (E)-1,2-bis[1-amino-1-(cyanoimino)-2-methyl-propan-2-yl]diazene 1,2-dioxide. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 441–447, March, 2006.     

Comparative Evaluation of CE and HPLC for Determination of Cotinine in Human Urine

Two rapid and popular methods—capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) have been compared for analysis of cotinine in human urine. Cotinine was analyzed in less than 7 min, with detection limits of 5 and 3.2 ng mL⁻¹ for CE and HPLC, respectively. The performance of the methods was evaluated in terms of sensitivity, specificity, precision, accuracy, and limits of detection and quantification. Calibration plots were linear in the range 50–4,000 ng mL⁻¹, at least, and mean recoveries were satisfactory for both techniques. The methods were successfully used for quantification of cotinine in urine.     

Theoretical investigation of 1,4-dioxane complexes with water in the <Emphasis Type="Italic">chair</Emphasis> conformation by semiempiric MNDO/PM3 method

The structure and relative stability of 1,4-dioxane-water, (Diox)_n·(H₂O )_m (n = 1, 2, m = 1–6), molecular complexes have been calculated by semiempirical MNDO/PM3 method. A considerable variety of (Diox)_n·(H₂O )_m isomeric structures was stated. The mean energy of O_Diox…H_W-O_W hydrogen bond in (Diox)_n·(H₂O)_m complexes formed by 1,4-dioxane molecules in the chair conformation amounts to ?2.293 ± 0.210 kcal/mol with the average bond length 2.797 0.015 Å.     

Synthesis, characterization and antifungal activity of copper (II) complexes of sterically hindered o-diphenol derivatives

Cu (II) complexes with 3,5-di(tert-butyl)-1,2-benzenediol (I), 4,6-di(tert-butyl)-1,2,3-benzentriol (II) and sulfur-containing sterically hindered o-diphenol derivatives such as 4,6-di(tert-butyl)-3-(2-hydroxyethylsulfanyl)-1,2-benzenediol (III) and 2-[4,6-di(tert-butyl)-2,3-dihydroxyphenylsulfanyl]acetic acid (IV) have been synthesized and characterized by means of elemental analysis, TG/DTA, FT-IR, ESR, XPS, XPD and conductivity measurements. Antifungal activities of these ligands and their respective Cu (II) complexes have been determined against Aspergillus niger, Fusarium sp., Penicillium lividum, Mucor sp. and Botrytis cinerea. Most of the compounds (both the free ligands and the complexes) exert pronounced antifungal activities (RI  70%), and virtually all of them (apart from the Cu(L^II)₂ complex) have the highest inhibitory properties (RI = 100%) against B. cinerea.     

X-Ray Investigation of Chiral β-Hydroxyketone Derived From (+)-Isomenthone

X-ray analysis was carried out to study the molecular structure of β-hydroxyketone, which is one of the minor products of selective aldol condensation of (−)-menthone with 4-carbomethoxybenzaldehyde. The cyclohexanone ring of the compound has a practically undistorted chair conformation with an axial orientation of the 1-methyl group and the bulkiest 2-[1′-hydroxy-1′ -(4-carbomethoxyphenyl)]methyl substituent and the equatorial orientation of the isopropyl group in the 4 position. The stereochemical configuration was found to be (1R,2R,4 R, 1′ S), supporting that the compound belongs to the group of (+)-isomenthones; i.e., the starting (-)-menthone undergoes (to a certain extent) epimerization under the reaction conditions used. In crystal, there is intermolecular hydrogen bonding >C=O...HO- (the -O...H- bond length is 2.15 Å). The molecular conformation in hydroxyketone crystals differs from the one which prevails in solutions (according to previous NMR data) and which is characterized by an inverted cyclohexanone ring and intramolecular hydrogen bonding >C=O...HO.Original Russian Text Copyright © 2004 by S. V. Shishkina, T. G. Drushlyak, L. A. Kutulya, N. S. Pivnenko, and O. V. Shishkin__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 5, pp. 933–940, September–October, 2004.     

Preservation of sensitive CRMs and monitoring their stability at IRMM

Over the years, the nature of CRMs has changed considerably. Recently, more and more CRMs have been certified in their "natural" form, that is processed as little as possible, with analytes at their natural concentration level. This and the trend towards certified properties other than the concentrations of clearly defined molecules/elements have made guaranteeing stability of CRMs and estimating a shelf life an even more important issue for reference material producers than it has been before. One way to meet this challenge is to take more care in processing, storage and dispatch of CRMs. At IRMM, approximately 20 % of the RMs are stored at –20 °C or below and about 10% require cooled transportation. In addition, increased efforts for assessing stability are needed. Shelf lives are estimated using addition of an uncertainty component based on real-temperature stability studies rather than by accelerated stability studies. These pre-certification efforts are complemented by a stability-monitoring program, which at IRMM includes 80 % of the non-nuclear and non-isotopic materials. Although the costs for these efforts are high in absolute terms, they are only a minor and indispensable contribution to the total costs of CRM production.     

Multiple binding modes of the camptothecin family to DNA oligomers

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].     

Synthesis, structure, and electrochemical properties of 12,42-dioxo-21,31-diphenyl-7,10,13-trioxa-1,4(3,1)-diquinoxalina-2(2,3),3(3,2)-diindolizinacyclopentadecaphane

The oxidative dehydrocyclization of the 3-(indolizin-2′-yl)-2-oxoquinoxaline monopodand performed either electrochemically or under the action of molecular iodine affords new redox-active heterocyclophane consisting of the redox-switchable biindolizine fragment combined with the polyether-bridged π-deficient quinoxaline systems. The single-crystal X-ray diffraction study showed that the trioxaundecane chain of heterocyclophane adopts an extended conformation, and one of the phenyl substituents of the molecule closes the pseudocavity formed by the spacer from one of the sides. The cyclic voltammetric study of heterocyclophane in MeCN and DMF showed the three-step oxidation of the indolizine fragments accompanied by the single-electron transfer in each step. The first and third steps are reversible, and the second step is irreversible. The oxidation at potentials of the first peak gives rise to stable radical cations detected by the ESR method (g = 2.0024, a _2N = 0.26 mT). Dedicated to Professor E. A. Berdnikov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1991–2003, October, 2007.