Surface wrinkling: the phenomenon causing bees in bitumen

The so called “bee phenomenon” in bitumen has been investigated by means of AFM quantitative nanomechanical property mapping. Bees are a phenomenon that can be observed by topography measurements using AFM. The characteristic “bee” appearance comes from regions with alternating higher and lower bands in the surface topography of bitumen, which are surrounded by a flat area. The proposed mechanism for bee formation is phase separation and differential contraction during cooling from melt temperatures leading to wrinkling due to differences in the elastic modulus of the material phases. Using a laminate wrinkling model, the thickness of the bee laminate was calculated from the wavelengths and Young’s moduli of the bee laminate and the matrix. It was found to vary between 70 and 140 nm for the five bitumen samples that contained significant amounts of wax.     

Synthesis and biological properties of novel pyridinioalkanoyl thiolesters (PATE) as anti-HIV-1 agents that target the viral nucleocapsid protein zinc fingers

Nucleocapsid p7 protein (NCp7) zinc finger domains of the human immunodeficiency virus type 1 (HIV-1) are being developed as antiviral targets due to their key roles in viral replication and their mutationally nonpermissive nature. On the basis of our experience with symmetrical disulfide benzamides (DIBAs; Rice et al. Science 1995, 270, 1194-1197), we synthesized and evaluated variants of these dimers, including sets of 4,4'- and 3,3'-disubstituted diphenyl sulfones and their monomeric benzisothiazolone derivatives (BITA). BITAs generally exhibited diminished antiviral potency when compared to their disulfide precursors. Novel, monomeric structures were created by linking haloalkanoyl groups to the benzamide ring through -NH-C(=O)- (amide) or -S-C(=O)- (thiolester) bridges. Amide-linked compounds generally lacked antiviral activity, while haloalkanoyl thiolesters and non-halogen-bearing analogues frequently exhibited acceptable antiviral potency, thus establishing thiolester benzamides per se as a new anti-HIV chemotype. Pyridinioalkanoyl thiolesters (PATEs) exhibited superior anti-HIV-1 activity with minimal cellular toxicity and appreciable water solubility. PATEs were shown to preferentially target the NCp7 Zn finger when tested against other molecular targets, thus identifying thiolester benzamides, and PATEs in particular, as novel NCp7 Zn finger inhibitors for in vivo studies.     

Evaluation of selected chemotypes in coupled cellular and molecular target-based screens identifies novel HIV-1 zinc finger inhibitors

Conservation of the Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys retroviral zinc finger sequences and their absolute requirement in both the early and late phases of retroviral replication make these chemically reactive structures prime antiviral targets. We recently reported that select 2,2'-dithiobisbenzamides (DIBAs) chemically modify the zinc finger Cys residues, resulting in release of zinc from the fingers and inhibition of HIV replication. In the current study we surveyed 21 categories of disulfide-based compounds from the chemical repository of the National Cancer Institute for their capacity to act as retroviral zinc finger inhibitors. Aromatic disulfides that exerted anti-HIV activity tended to cluster in the substituted aminobenzene, benzoate, and benzenesulfonamide disulfide subclasses. Only one thiuram derivative exerted moderate anti-HIV activity, while a number of nonaromatic thiosulfones and miscellaneous disulfide congeners were moderately antiviral. Two compounds (NSC 20625 and NSC 4493) demonstrated anti-cultures. The two compounds chemically modified the p7NC zinc fingers in two separate in vitro assays, and interatomic surface molecular modeling docked the compounds efficiently but differentially into the zinc finger domains. The combined efforts of rational drug selection, cell-based screening, and molecular target-based screening led to the identification of zinc finger inhibitors that can now be optimized by medicinal chemistry for the development of biopharmaceutically useful anti-HIV agents.     

Stabilization of PACREL® by organotellurium compound

The addition of 0.17–0.50% of bis[4-(dimethylamino)phenyl]telluride to the thermoplastic elastomer PACREL^® significantly improved tensile strength and elongation at break in unaged and oven-aged samples. Chemiluminescence measurements showed that the organotellurium compound considerably prolonged the induction period of thermooxidation of the material and drastically reduced the total luminescence intensity of unaged and aged samples. These results indicate that the improved mechanical properties of diaryl telluride stabilized PACREL^® can be attributed to the antioxidative (peroxide decomposing, chain breaking) properties of the stabilizer. © 1998 John Wiley & Sons, Inc. J. Appl. Polym. Sci. 70: 449–556, 1998     

Structural investigation of C4b-binding protein by molecular modeling: localization of putative binding sites

C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one beta-chain and seven alpha-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its alpha-chains and with protein S through its beta-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP alpha-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the alpha-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions.     

Can computationally designed protein sequences improve secondary structure prediction?

Computational sequence design methods are used to engineer proteins with desired properties such as increased thermal stability and novel function. In addition, these algorithms can be used to identify an envelope of sequences that may be compatible with a particular protein fold topology. In this regard, we hypothesized that sequence-property prediction, specifically secondary structure, could be significantly enhanced by using a large database of computationally designed sequences. We performed a large-scale test of this hypothesis with 6511 diverse protein domains and 50 designed sequences per domain. After analysis of the inherent accuracy of the designed sequences database, we realized that it was necessary to put constraints on what fraction of the native sequence should be allowed to change. With mutational constraints, accuracy was improved vs. no constraints, but the diversity of designed sequences, and hence effective size of the database, was moderately reduced. Overall, the best three-state prediction accuracy (Q(3)) that we achieved was nearly a percentage point improved over using a natural sequence database alone, well below the theoretical possibility for improvement of 8-10 percentage points. Furthermore, our nascent method was used to augment the state-of-the-art PSIPRED program by a percentage point.     

Topological studies of the amino terminal modules of vitamin K-dependent protein S using monoclonal antibody epitope mapping and molecular modeling

Neglected fractures of the femoral neck, common in young adults in underdeveloped countries, may be complicated by nonunion or avascular necrosis (AVN). We treated 52 cases by open reduction, fixation by compression screw and a free fibular graft. The mean delay between injury and operation was 5.1 months. Of 40 fractures assessed at a mean of 58.8 months (24 to 153), 38 were found to be united and two, owing to surgical errors, were not. Seven of eight heads which were avascular before operation revascularised without collapse, while seven others developed AVN after the procedure. At the last follow-up considerable collapse was apparent in five femoral heads, and 11 hips had developed coxa vara. The fibular graft had fractured in four cases. The hip had been penetrated by the screw in six cases and by the graft in three. Hip function was excellent in seven patients, good in 21 and fair in seven. Five patients had poor results. Incorporation of the fibular graft was seen after four years: in many cases the graft had been almost completely resorbed. We recommend this procedure for the treatment of neglected fractures of the neck of the femur in young adults to reduce resorption of the neck, AVN and nonunion.     

Simplified amino acid alphabets for protein fold recognition and implications for folding

Protein design experiments have shown that the use of specificsubsets of amino acids can produce foldable proteins. This promptsthe question of whether there is a minimal amino acid alphabetwhich could be used to fold all proteins. In this work we makean analogy between sequence patterns which produce foldablesequences and those which make it possible to detect structuralhomologs by aligning sequences, and use it to suggest the possiblesize of such a reduced alphabet. We estimate that reduced alphabetscontaining 10–12 letters can be used to design foldablesequences for a large number of protein families. This estimateis based on the observation that there is little loss of theinformation necessary to pick out structural homologs in a clusteredprotein sequence database when a suitable reduction of the aminoacid alphabet from 20 to 10 letters is made, but that this informationis rapidly degraded when further reductions in the alphabetare made.