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Electrostatic Interaction Energies (electrostatic + interaction_energy)
Selected AbstractsThe interplay between experiment and theory in charge-density analysisACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2004Philip Coppens The comparison of theory and experiment remains a cornerstone of scientific inquiry. Various levels of such comparison applicable to charge-density analysis are discussed, including static and dynamic electron densities, topological properties, d -orbital occupancies and electrostatic moments. The advantages and drawbacks of the pseudoatom multipole are discussed, as are the experimentally constrained wavefunctions introduced by Jayatilaka and co-workers, which combine energy minimization with the requirement to provide a reasonable fit to the X-ray structure factors. The transferability of atomic densities can be exploited through construction of a pseudoatom databank, which may be based on analysis of ab initio molecular electron densities, and can be used to evaluate a host of physical properties. Partitioning of theoretical energies with the Morokuma,Ziegler energy decomposition scheme allows direct comparison with electrostatic interaction energies obtained from electron densities represented by the pseudoatom formalism. Compared with the Buckingham expression for the interaction between non-overlapping densities, the agreement with theory is much improved when a newly developed hybrid EP/MM (exact potential/multipole model) method is employed. [source] Do electrostatic interactions destabilize protein,nucleic acid binding?BIOPOLYMERS, Issue 2 2007Sanbo Qin Abstract The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter-intuitive when previous Poisson,Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein,nucleic acid binding. Our own PB calculations on protein,protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein,protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein,RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 112,118, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Effects of Ionic Environments on Bovine Serum Albumin Fouling in a Cross-Flow Ultrafiltration SystemCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 2 2007S. Salg Abstract The influence of electrostatic interactions on membrane fouling during the separation of bovine serum albumin (BSA) from solution was studied in a cross-flow ultrafiltration system. Experiments were carried out at different pH values between 3.78 and 7.46; and for different ionic strengths between 0.001,M and 0.1,M. The changes in permeate flux, cake layer resistance, zeta potentials of BSA and polyether sulfone (PES) membranes, and electrostatic interaction energies, were evaluated. At all of the ionic conditions studied, PES membranes are negatively charged. However, BSA molecules are either negatively or positively charged depending on the ionic environment. Whereas the cake layer resistance decreased with increasing pH and ionic strength, the permeate fluxes increased. The calculated electrostatic energy was a minimum at the isoelectric point (IEP) of BSA. However, at this point, the cake resistances corresponding to fouling at each ionic strength, were not minimized. Below the IEP of BSA, the electrostatic forces were attractive, while above the IEP, repulsive electrostatic forces were dominant. [source] Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic siteJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2005Hirofumi Fujimoto Abstract Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8-oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 788,798, 2005 [source] Experimental charge-density study of paracetamol , multipole refinement in the presence of a disordered methyl groupACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009Joanna M. B A high-resolution single-crystal X-ray study of paracetamol has been performed at 85,K. Different approaches to modeling the experimental electron density (ED) were tested for the dynamically disordered portions of the molecule in order to check to what extent it is possible to obtain a proper ED distribution in the ordered part. Models were examined in which the methyl-group ED was built from pseudoatoms taken from the University at Buffalo Pseudoatom Databank or the Invariom database, with multipole parameters for the remaining atoms being obtained from free refinement. The ,, restricted multipolar model (KRMM) and free ,, refinements were compared; restriction of the ,, parameters was essential in order to obtain values of the electrostatic interaction energy consistent with the results of theoretical single-point periodic calculations. After simultaneous use of KRMM refinement and the databases to model the methyl group, the bond critical point properties and interaction electrostatic energy values were found to be closer to those obtained from theory. Additionally, some discrepancies in the ED distribution and dipole moment among transferred aspherical atom model refinements utilizing both theoretical databases and parameters from theoretical periodic calculations are shown. Including the influence of the crystal field in the periodic calculations increases the ED in the hydroxyl and amide groups, thus leading to higher values of the electrostatic interaction energy, changes in the electrostatic potential values mapped on the isodensity surface and changes in the shape of the anisotropic displacement parameters with respect to results found for both database models. [source] Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme,substrate complex: influenza neuraminidase inhibitionACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Paulina M. Dominiak Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (,,300,kJ,mol,1 for ,COO, in non-aromatic inhibitors, ,,120,210,kJ,mol,1 for ,COO, in aromatic inhibitors and ,,450,kJ,mol,1 for ,PO32,) and with the amino and guanidine groups at C4 (,,250,kJ,mol,1). Other groups contribute less than ,100,kJ,mol,1. Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292,Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing inhibitors compared with the more hydrophobic derivatives. [source] | ||||||||||