Search results for "interaction [dark matter]"
showing 10 items of 363 documents
Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent
2013
Human 70 kDa heat shock protein (hHsp70) is an ATP-dependent chaperone and is currently an important target for developing new drugs in cancer therapy. Knowledge of the conformations of hHsp70 is central to understand the interactions between its nucleotide-binding domain (NBD) and substrate-binding domain (SBD) and is a prerequisite to design inhibitors. The conformations of ADP-bound (or nucleotide-free) hHsp70 and ATP-bound hHsp70 was investigated by using unbiased all-atom molecular dynamics (MD) simulations of homology models of hHsp70 in explicit solvent on a timescale of .5 and 2.7 μs, respectively. The conformational heterogeneity of hHsp70 was analyzed by computing effective free-e…
Novel structural insights into F-actin-binding and novel functions of calponin homology domains.
2008
Tandem calponin homology (CH) domains are well-known actin filaments (F-actin) binding motifs. There has been a continuous debate about the details of CH domain-actin interaction, mainly because atomic level structures of F-actin are not available. A recent electron microscopy study has considerably advanced our structural understanding of CH domain:F-actin complex. On the contrary, it has recently also been shown that CH domains can bind other macromolecular systems: two CH domains from separate polypeptides Ncd80, Nuf2 can form a microtubule-binding site, as well as tandem CH domains in the EB1 dimer, while the single C-terminal CH domain of alpha-parvin has been observed to bind to a alp…
Emotions, Motives, Individuals, and Cultures in Interaction
2016
Cognitive aspects of the human mind form the foundations of solving usability problems. However, being able to use a technology is not the only critical psychological question in the design of successful HTI. In addition to understanding users’ capabilities, it is equally important to comprehend their preferences and what they want to accomplish with the help of technologies. Knowledge of the dynamic mind—in particular human emotions, motives, and personality—helps address such ‘liking and wanting’ concerns in HTI design.
Modelling of natural synthetic polyelectrolyte interactions in natural waters by using SIT, Pitzer and Ion Pairing approaches
2006
Abstract In this paper SIT and Pitzer models are used for the first time to describe the interactions of natural and synthetic polyelectrolytes in natural waters. Measurements were made potentiometrically at 25 °C in single electrolyte media, such as Et 4 NI and NaCl (for fulvic acid 0.1 − 1 S single salt ” BA, with cation B and anion A representing all the major cations (Na + , K + , Mg 2+ , Ca 2+ ) and anions (Cl − , SO 4 2− ) in natural sea water, respectively. The ion pair formation model was also applied to fulvate and alginate in artificial sea water by examining the interaction of polyanions with the single sea water cation. Results were compared with those obtained from previous sp…
Interaction of 5‐fluorouracil with β‐cyclodextrin: A density functional theory study with dispersion correction
2020
Detailed studies on the stability, interaction, and microstructure of host‐guest complexes in the vacuum of 5‐fluorouracil (5FU) with β‐cyclodextrin (βCD) were performed using B3LYP with the inclusion of Grimme's dispersion correction GD3 term and 6‐31+G(d,p) basis set. Among several studied 1:1 5FU‐βCD complexes, the one placing the keto tautomer of 5FU vertically in the host cavity and forming N‐H···OCD and CO···HOCD hydrogen bonds with hydroxyl groups of the smaller rim of βCD has the highest stability (Eint = −195 kJ/mol). Interestingly, there are no interactions with the inner hydrophobic part of the βCD host cavity. The strength of the intermolecular H‐bonds to the smaller rim of βC…
Controlling the wetting properties of the Asakura-Oosawa model and applications to spherical confinement.
2012
We demonstrate for the Asakura-Oosawa model and an extension of this model that uses continuous rather than hard potentials, how wetting properties at walls can be easily controlled. By increasing the interaction range of the repulsive wall potential acting on the colloids (while keeping the polymer-wall interactions constant) polymers begin to substitute colloids at walls and the system can be driven from complete wetting of colloids via partial wetting to complete wetting of polymers. As an application, we discuss the morphology and wetting behavior of colloid-polymer mixtures in spherical confinement. We apply the recently developed 'ensemble switch method' where the Hamiltonian is exten…
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
2007
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…
Estimation of pKa shifts in weak polyacids using a simple molecular model: effects of strong polybases, hydrogen bonding and divalent counterion bind…
2004
Abstract The pKa values of ionizable groups in macromolecules can be significantly different than those of the isolated groups in solution. We have estimated theoretically the changes in the dissociation constant of a weak acid (a) in the vicinity of another ionizable group (b) on the basis of the theoretical approach by Hill (J. Am. Chem. Soc. 78 (1956) 3330) for matching pairs of interacting sites on two large molecules. Three cases are considered for group b: the strong base, the same weak acid as group a with hydrogen bonding between them, and the same weak acid as group a with divalent counterion binding. The pKa shifts are evaluated in each case as a function of the interaction energy…
Interactions between polymer brush-coated spherical nanoparticles: the good solvent case.
2011
The interaction between two spherical polymer brushes is studied by molecular dynamics simulation varying both the radius of the spherical particles and their distance, as well as the grafting density and the chain length of the end-grafted flexible polymer chains. A coarse-grained bead-spring model is used to describe the macromolecules, and purely repulsive monomer-monomer interactions are taken throughout, restricting the study to the good solvent limit. Both the potential of mean force between the particles as a function of their distance is computed, for various choices of the parameters mentioned above, and the structural characteristics are discussed (density profiles, average end-to…
Can one detach a fully adsorbed flexible polymer chain by an ultra-small external force?
2013
Full adsorption of flexible chains onto typical solid substrates occurs at a surface interaction energy of (5–10) kBT. The corresponding detachment force is in the range 10–50 pN. In contrast to “bare” solid substrates common to non-living materials, surfaces coated with brush-like polymer layers are very common in biological soft matter. We employ a simple mean-field approach to describe the effects of weak attraction between a floating long macromolecule and the brush. We show that even for a moderately thick brush a very small effective attraction is enough to produce complete binding of the long chain. The detachment force scales as , where W is the brush thickness. Hence the force coul…