Molecular modelling of the mass density of single proteins

Using molecular dynamics (MD) simulations, the density of single proteins and its temperature dependence was modelled starting from the experimentally determined protein structure and a generic, transferable force field, without the need of prior parameterization. Although all proteins consist of the same 20 amino acids, their density in aqueous solution varies up to 10% and the thermal expansion coefficient up to twofold. To model the protein density, systematic MD simulations were carried out for 10 proteins with a broad range of densities (1.32–1.43?g/cm³) and molecular weights (7–97?kDa). The simulated densities deviated by less than 1.4% from their experimental values that were available for four proteins. Further analyses of protein density showed that it can be essentially described as a consequence of amino acid composition. For five proteins, the density was simulated at different temperatures. The simulated thermal expansion coefficients ranged between 4.3 and 7.1?×?10^?4?K^?1 and were similar to the experimentally determined values of ribonuclease-A and lysozyme (deviations of 2.4 and 14.6%, respectively). Further analyses indicated that the thermal expansion coefficient is linked to the temperature dependence of atomic fluctuations: proteins with a high thermal expansion coefficient show a low increase in flexibility at increasing temperature. A low increase in atomic fluctuations with temperature has been previously described as a possible mechanism of thermostability. Thus, a high thermal expansion coefficient might contribute to protein thermostability.     

Evidence for a credit-card-swipe mechanism in the human PC floppase ABCB4

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Investigating the Mechanistic Inhibitory Discrepancies of Novel Halogen and Alkyl Di-Substituted Oxadiazole-Based Dibenzo-Azepine-Dione Derivatives on Poly (ADP-Ribose) Polymerase-1

Numerous studies have established the involvement of Poly (ADP-ribose) Polymerase-1 (PARP-1) in cancer presenting it as an important therapeutic target over recent years. Although homology among the PARP protein family makes selective targeting difficult, two compounds [d11 (0.939 μM) and d21 (0.047 μM)] with disparate inhibitory potencies against PARP-1 were recently identified. In this study, free energy calculations and molecular simulations were used to decipher underlying mechanisms of differential PARP-1 inhibition exhibited by the two compounds. The thermodynamics calculation revealed that compound d21 had a relatively higher ΔG_bind than d11. High involvement of van der Waal and electrostatic effects potentiated the affinity of d21 at PARP-1 active site. More so, incorporated methyl moiety in d11 accounted for steric hindrance which, in turn, prevented complementary interactions of key site residues such as TYR889, MET890, TYR896, TYR907. Conformational studies also revealed that d21 is more stabilized for interactions in the active site compared to d11. We believe that findings from this study would provide an important avenue for the development of selective PARP-1 inhibitors.     

Biochemical characterization of activation-associated bovine class I major histocompatibility complex antigens

Summary. Utilizing a 'sandwich' ELISA assay we have been able to demonstrate that mAb W6/32, B1G6 and IL-A19 are reactive with three different monomorphic determinants on bovine class I major histocompatibility complex (MHC) molecules. Sequential immunoprecipitations performed with the mAb revealed that class I molecules on PBM comprise a single population with respect to reactivity with the mAb in that the β2m-associated proteins bear all three epitopes. By contrast, TCGF-driven lymphoblasts and cells transformed by Theileria parva (Tp) additionally express molecules of Mr 45000 bound to β2m which are recognized by mAb B1G6 and IL-A19 but not by W6/32. These two subclasses of molecules were further distinguished on the basis that, when tunicamycin was added to cultures in the preparation of cells for analysis, mAb W6/32 precipitated class I heavy chains of Mr 39000 while the extra molecules detected only by mAb B1G6 and IL-A19 were of Mr 37000 and 39000. On thymocytes, the mAb W6/32-non-reactive class I molecules are present in low amounts and are expressed by cells in the medulla area, unlike BoT1 (analogous to human CD1) molecules which are expressed by the cortical cells. Our studies also revealed that the supposed β2m-specific mAb B1G6 does not recognize the β2m-associated molecules (BoT1) precipitated by mAb TH97A and thus the specificity of mAb B1G6 in cattle is for an epitope on bovine β2m which is strongly influenced by the nature of the heavy chain with which the β2m is associated.     

Host kairomone learning and foraging success in an egg parasitoid: a simulation model

Abstract 1. Trissolcus basalis (Wollaston) (Hymenoptera: Scelionidae) is an egg parasitoid that recognises chemical residues left by its host the green stink bug Nezara viridula (L.) (Heteroptera: Pentatomidae) as kairomone signals, enabling it to find egg masses in which to lay eggs. 2. Kairomones are usually present as patches deposited by N. viridula females, and recent results (Peri et al., Journal of Experimental Biology, 209 , 3629–3635, 2006) indicated that females of T. basalis are able to learn the features of their foraging environment and to adjust accordingly the amount of time spent on the patches of kairomones they are visiting, depending on whether or not host eggs are found. 3. In order to assess the impact of this learning ability, a Monte Carlo, spatially explicit and individual‐based simulation model was built to quantify the foraging efficiency of T. basalis females in environments with different levels of host abundance and distribution. In all cases, the present study compared the foraging efficiency of simulated T. basalis females having the ability to learn with those lacking this ability. 4. Learning females always visited a higher number of kairomone patches and attacked a higher number of hosts than non‐learning females, especially when there was a high density of kairomone patches in the environment. 5. Learning ability globally appears to allow the maintenance of efficient foraging success, especially when there is a low probability for the kairomone patches to contain discoverable hosts. 6. The increase in foraging efficiency for learning females appears to depend on the characteristics of the habitat in which they are foraging. Results thus suggest that significant variation in learning ability is likely to occur in natural wasp populations facing different environments with different host spatial distributions.     

Direct numerical simulation of expiratory crackles: Relationship between airway closure dynamics and acoustic fluctuations

This paper investigates the relationship between airway closure dynamics and acoustic fluctuations in expiratory crackles using direct numerical simulation. A unified mathematical model is proposed to deal with flow in an airway, elastic deformation of the airway wall, surface tension driven motion of the liquid film that lines the airway, and their acoustic fluctuations because of material compressibility. Airway closure is induced by increasing the surrounding pressure, then the source of the pressure fluctuations is measured over time. Our results show that the airway closure occurs suddenly because of a bridge formation of the liquid film, and high energy transfer occurs between the kinetic energy, the surface energy of the liquid interface, and the elastic energy of the airway wall, invoking a large acoustic fluctuation that causes the expiratory crackles. Nonlinear behavior is observed in terms of the airway wall stiffness; the dynamic motion of the airway closure becomes moderate and both the energy transfer and acoustic fluctuations are dramatically reduced with an increase in airway wall stiffness.     

Molecular dynamics of human alpha-fetoprotein fragment LDSYQCT and its analogs at different dielectric constants

A comparative study of the conformation dynamics of the human alpha-fetoprotein fragment LDSYQCT and heptapeptides derived from it by point substitutions has revealed a significant influence of electrostatic interactions on the set of preferred conformations and dynamics of amino acid residues when the peptides with blocked termini are examined at ? = 1. Peptide flexibility rises when the termini are left free (charged). At ? = 10 or 80, the set of probable conformations for all residues expands to much the same extent, i.e., at higher permittivity of the medium the dynamic effects of amino acid changes are leveled off.