Molecular Modeling Predictions Research Articles

Molecular modelling and epitope prediction of gp29 from lymphatic filariae

The sequence of the major soluble protein component of the cuticle of filarial nematodes is homologous to that of bovine glutathione peroxidase, for which an X-ray structure is available. Due to the high degree of sequence identity (42%), it has been possible to build an apparently reliable three-dimensional model of the gp29 cuticular protein from Brugia spp. that will aid studies of the molecule both as a target immunogen and secreted enzyme. The modelled core of the gp29 structure is conserved compared to the bovine enzyme, consisting of aβ-sheet surrounded by α-helices. Experimental data showed that Brugia spp. gp29 has four subunits, and a tetrameric form of gp29 has also been modelled. The two N-linked glycosylation sites per subunit were predicted to lie on the surface of the tetramer. Most of the variation in amino acid sequence compared to that of mammalian enzymes, occurs in the surface loops, several of which are larger and more exposed in gp29. Deglycosylated gp29 was demonstrated to be immunogenic in human infection, and six likely B-cell epitopes have been predicted on the basis of a high protrusion index and sequence variability.

Effect of terminal nonhomologies on homologous recombination in Xenopus laevis oocytes.

Homologous recombination of linear DNA molecules in Xenopus laevis oocytes is very efficient. The predictions of molecular models for this recombination process were tested with substrates with terminal nonhomologies (nonhomologous sequences). It was found that nonhomologies on one or both ends of an otherwise efficient substrate substantially reduced the yield of recombination products. In the case of a single nonhomology, inhibition was observed for all lengths of nonhomology, from 60 to 1,690 bp, being most dramatic for the longer blocks. Examination of time courses of recombination showed that the blocks were largely kinetic; that is, substrates with short nonhomologies eventually yielded substantial levels of completed products. Intermediates that accumulated after the injection of end-blocked substrates were characterized by two-dimensional gel electrophoresis and hybridization with strand-specific oligonucleotide probes. These blocked intermediates were shown to have base-paired junctions, but resolution was prevented by the failure to remove the 3'-ending strand of the original nonhomology. Continuing exonuclease action created a single-strand gap adjacent to the position of the persistent nonhomology. In contrast, the strand that included the unblocked side of the junction could be sealed. These results are consistent with a nonconservative, resection-annealing mechanism of homologous recombination in the oocytes and suggest the absence of any activity that can efficiently remove 3' tails.

Effect of terminal nonhomologies on homologous recombination in Xenopus laevis oocytes.

Homologous recombination of linear DNA molecules in Xenopus laevis oocytes is very efficient. The predictions of molecular models for this recombination process were tested with substrates with terminal nonhomologies (nonhomologous sequences). It was found that nonhomologies on one or both ends of an otherwise efficient substrate substantially reduced the yield of recombination products. In the case of a single nonhomology, inhibition was observed for all lengths of nonhomology, from 60 to 1,690 bp, being most dramatic for the longer blocks. Examination of time courses of recombination showed that the blocks were largely kinetic; that is, substrates with short nonhomologies eventually yielded substantial levels of completed products. Intermediates that accumulated after the injection of end-blocked substrates were characterized by two-dimensional gel electrophoresis and hybridization with strand-specific oligonucleotide probes. These blocked intermediates were shown to have base-paired junctions, but resolution was prevented by the failure to remove the 3'-ending strand of the original nonhomology. Continuing exonuclease action created a single-strand gap adjacent to the position of the persistent nonhomology. In contrast, the strand that included the unblocked side of the junction could be sealed. These results are consistent with a nonconservative, resection-annealing mechanism of homologous recombination in the oocytes and suggest the absence of any activity that can efficiently remove 3' tails.

Environmental fatigue of an Al-Li-Cu alloy: part I. Intrinsic crack propagation kinetics in hydrogenous environments

Deleterious environmental effects on steady-state, intrinsic fatigue crack propagation (FCP) rates(da/dN) in peak-aged Al-Li-Cu alloy 2090 are established by electrical potential monitoring of short cracks with programmed constant ΔK andKmaxI loading. Such rates are equally unaffected by vacuum, purified helium, and oxygen but are accelerated in order of decreasing effectiveness by aqueous 1 pct NaCl with anodic polarization, pure water’ vapor, moist air, and NaCl with cathodic polarization. Whileda/dN depend on ΔK4.0 for the inert gases, water vapor and chloride induce multiple power laws and a transition growth rate “plateau.” Environmental effects are strongest at low ΔK. Crack tip damage is ascribed to hydrogen embrittlement because of acceleratedda/dN due to parts-per-million (ppm) levels of H2O without condensation, impeded molecular flow model predictions of the measured water vapor pressure dependence ofda/dN as affected by mean crack opening, the lack of an effect of film-forming O2, the likelihood for crack tip hydrogen production in NaCl, and the environmental and ΔK-process zone volume dependencies of the microscopic cracking modes. For NaCl, growth rates decrease with decreasing loading frequency, with the addition of passivating Li2CO3 and upon cathodic polarization. These variables increase crack surface film stability to reduce hydrogen entry efficiency. Small crack effects are not observed for 2090; such cracks do not grow at abnormally high rates in single grains or in NaCl and are not arrested at grain boundaries. The hydrogen environmental FCP resistance of 2090 is similar to other 2000 series alloys and is better than 7075.

Parameter relation rows: a query system for protein structure function relationships

In the course of molecular modeling or mutant prediction one often wants quick answers to questions such as: 'Are there any residues in a beta-strand that point into an internal cavity, and are highly mutable?' 'Are there large polar residues in a helix that make a contact with a hydrophobic residue in a sheet, and don't make the maximal number of hydrogen bonds?' or 'Which hydrophobic residues are in a helix with a large hydrophobic moment, and make a contact with a co-factor, but at the same time still have a large accessible surface?'. I describe here a method to get answers to these kinds of questions in a very quick and easy manner. The method described is partly based on the principles used in the design of relational databases, and its mode of operation is similar to the query methods used in a relational database environment. Although designed for aiding in molecular modeling, its applicability is much more general. The method has been implemented as part of a large molecular modeling package which copes with the numerous problems in systematic handling of protein structures, e.g. residue numbering. This also implies that many normal tools such as graphical analyses, I/O facilities, etc. are available on-line.

Separated projectile and targetK x-ray production in symmetric heavy ion collisions as a function of the target thickness

Cross sections for projectile and targetK x-ray emission have been measured as a function of the target thickness for the symmetric systems Ni-Ni, Cu-Cu, Nb-Nb, Ag-Ag at energies between 75 and 105 MeV. The projectileK x-rays were separated from the target ones by using the Doppler shift. Kα and Kβ energy shifts and Kβ to Kα intensity ratios were also determined and used to calculateM- andL-ionization and the correspondingK-fluorescence yield for both collision partners. At non vanishing small target thicknesses, the targetK-vacancy production cross section is generally larger than that of the projectile. By analysing the target thickness dependence of the cross sections with a two component model which takes also into account the evolution of the projectileM-,L- andK-shell population inside the solid, targetK-vacancy sharing and cross sections forKK electron capture in symmetric systems could be determined. These results are in good agreement with molecular orbital model predictions.

Rheo‐optical studies of concentrated polystyrene solutions subjected to transient simple shear flow

AbstractConcentrated polystyrene solutions were investigated on the inception and cessation of simple shear flow by means of the technique of two‐color flow birefringence. Both monodisperse solutions of various molecular weights and bimodal mixtures were studied. The molecular weight affected both the amount of overshoot in the birefringence and the response time on the inception of shear flow. Large overshoots in birefringence, up to 250%, and undershoot in the orientation angle were observed. The shear stress and the first normal stress difference were calculated by using the stress–optical rule. The amount of strain at the peaks in the stress growth curves are presented along with the steady‐state viscosity and primary normal stress coefficient. The experimental results are compared qualitatively with theoretical predictions of various molecular models.

A wide-angle X-ray study of the development of molecular orientation in crosslinked natural rubber

Molecular orientation parameters have been measured for the non-crystalline component of crosslinked natural rubber samples deformed in uniaxial tension as a function of the extension ratio and of temperature. The orientation parapeters 〈 P 2(cos α)〉 and 〈 P 4(cos α)〉 were obtained by an analysis of the anisotropy of the wide-angle X-ray scattering functions. For the measurements made at high temperatures the level of crystallinity detected was negligible and the orientation-strain behaviour could be compared directly with the predictions of molecular models of rubber elasticity. The molecular orientation behaviour with strain was found to be at variance with the estimates of the affine model particularly at low and moderate strains. Extension of the crosslinked rubber at room temperature led to strain-crystallization and measurements of both the molecular orientation of the non-crystalline chains and the degree of crystallinity during extension and relaxation enabled the role of the crystallites in the deformation process to be considered in detail. The intrinsic birefringence of the non-crystalline component was estimated, through the use of the 〈 P 2(cos α)〉 values obtained from X-ray scattering measurements, to be 0.20±0.02.

Small angle X-ray scattering measurements with dilute solutions of bovine fibrinogen

Data from small angle X-ray scattering measurements with dilute solutions of fibrinogen are presented; they are compared with the predictions of various molecular models suggested from studies with the electron microscope.