Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2.

Nematode anticoagulant proteins (NAPs) from the hematophagous nematode Ancylostoma caninum inhibit blood coagulation with picomolar inhibition constants, and have been targeted as novel pharmaceutical agents. NAP5 and NAP6 inhibit factor Xa by binding to its active site, whereas NAPc2 binds to factor Xa at a different, as yet unidentified, site and the resultant binary complex inhibits the tissue factor-factor VIIa complex. We have undertaken NMR studies of NAPc2, including the calculation of a solution structure, and found that the protein is folded, with five disulfide bonds, but is extremely flexible, especially in the acidic loop. The Halpha secondary shifts and 3JHNHalpha coupling constants indicate the presence of some beta structure and a short helix, but the intervening loops are highly conformationally heterogeneous. Heteronuclear NOE measurements showed the presence of large amplitude motions on a subnanosecond timescale at the N-terminus and C-terminus and in the substrate-binding loop, indicating that the conformational heterogeneity observed in the NMR structures is due to flexibility of the polypeptide chain in these regions. Flexibility may well be an important factor in the physiological function of NAPc2, because it must interact with other proteins in the inhibition of blood coagulation. We suggest that this inhibitor is likely to become structured on binding to factor Xa, because the inhibition of the tissue factor-factor VIIa complex requires both NAPc2 and factor Xa.     

The age distribution of cells in stratified squamous epithelium

In structured tissues such as stratified squamous epithelium the age distribution of cycling cells in a particular part of the tissue is influenced by cell migration. Age distributions are derived for the proliferative cells of stratified squamous epithelium, dependent on the mode of migration; and the effect of using analytical methods which assume exponential or rectangular age distributions is discussed with particular reference to the analysis of stathmokinetic experiments.     

A NOESY-HSQC simulation program, SPIRIT

A program SPIRIT (Simulation Program considering Incomplete Recovery of z magnetization and INEPT Transfer efficiency) has been developed to simulate three-dimensional NOESY-HSQC spectra. This program takes into account (1) different transfer efficiency during INEPT and reverse INEPT durations due to differential relaxation rates and¹ J coupling constants; (2) the different effect of the sensitivity-enhancement scheme on CH, CH₂ and CH₃ systems; and (3) incomplete recovery of longitudinal magnetization between scans. The simulation program incorporates anisotropic tumbling mode for symmetric tops, and allows for differential external relaxation rates for protons. Some well-defined internal motions, such as the fast rotation of methyl groups, are taken into account. The simulation program also allows for input of multiple conformations and their relative populations to calculate the average relaxation matrix to account for slow internal motions. With the SPIRIT program, the sensitivity-enhanced NOESY-HSQC experiment can be used directly in the evaluation of the accuracy of structures, which can potentially be improved by direct refinement against the primary data. Abbreviations: NOESY, nuclear Overhauser enhancement spectroscopy; HSQC, heteronuclear single quantum correlation; INEPT, insensitive nuclei enhanced by polarization transfer.     

The chromatin structure of Rous sarcoma proviruses is changed by factors that act in trans in cell hybrids.

In several lines of Rous sarcoma virus (RSV)-transformed rat cells the proviruses are in a configuration typical of active eukaryotic genes. They are sensitive to pancreatic DNase I, with sites hypersensitive to nuclease near the 5' end of the genome, they are close to the nuclear 'cage' and they show a low level of cytosine methylation in CpG doublets. In contrast, in phenotypically untransformed hybrids between these cells and uninfected rat or mouse cells, RSV inactivity is associated with hypermethylation of the provirus, reduced DNase I sensitivity (in two out of three examples) and, where examined, relative remoteness from the nuclear cage. These changes in proviral configuration, which occur rarely in spontaneous reversion of transformed cells, can thus be induced at high frequency and stability in cell hybrids by trans-acting influences of the uninfected parents.     

Flow cytometric determination of cell cycle phase-specific changes in cellular phosphatase and glycosidase activities

The activities of two phosphatases (E.C. 3.1.3.1 and 3.1.4.1) and four glycosidases (E.C. 3.2.1.21, 3.2.1.30, 3.2.1.31 and 3.2.1.51) were measured by fluorescence spectrophotometry, and flow cytometry, in mitogen-stimulated lymphocytes, and in cultures of Molt-4-F and F-89 cell lines, synchronized by hydroxyurea or thymidine. All enzymes were active throughout the cycle but the activities of three enzymes were elevated at specific points in the cycle, alkaline phosphatase activity increased at G2 + M/G1 boundary and in early S-phase, the activity of beta-L fucosidase was elevated in G1 and late S-phase. Orthophosphate diesterase activity was elevated at the G1/S boundary, and during G2 + M. The increase in beta-L fucosidase activity was due to an increased number of cells showing activity, whilst the increase in orthophosphate diesterase activity was attributable to an increase in cellular enzyme activity. Only the activities of orthophosphate diesterase and beta-L fucosidase were measurable by flow cytometry, alkaline phosphatase activity was mainly extracellular, and therefore not detectable by flow cytometric methods employed.     

Analysis and prediction of antibacterial peptides

Background  

Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacterial peptides, obtained from antimicrobial peptide database APD, in order to understand the preference of amino acid residues at specific positions in these peptides.