Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

A 3D-QSAR study using comparative molecular field analysis (CoMFA) was carried out on anti-tubulin agents with indole as a nucleus core. The structures of the compounds were obtained using docking calculations, and were then subjected to alignment procedures. CoMFA calculations for the 42 ligands that were examined as the training set gave a q2 value of 0.623 in correlation with experimental IC50 values for the inhibition of MKN-45 gastric cancer cells. Calculation for the test set of 17 ligands resulted in an r2 value of 0.714. The calculated results suggest that the R3 functional group site (see structure in Fig. 1) favored bulky groups while R1, R2, and R4 sites favored the opposite. At the R5 and R6 sites, parts of the region favored bulky groups while other parts favored the opposite. As for the electrostatic aspect, the R3 site was found to favor groups with a negative partial charge. At the R2 site, part of the region favored the group with a negative partial charge while other regions favored groups with a positive partial charge. The R4 and R5 sites favored groups with negative and positive partial charges, respectively, with a less favorable magnitude when compared with the R2 and R3 sites. The R1 and R6 sites did not exhibit significant electrostatic favor. Correlation of the results with IC50 values of ligands were analyzed and discussed.

Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.

Tryptophan is the largest amino acid found in proteins, with multiple functional roles. Its side-chain is made up of the hydrophobic indole moiety, with two groups acting as donors in hydrogen bonds: the Nε-H group, which is a potent donor in canonical hydrogen bonds; and a polarized Cδ1-H group, capable of forming weaker, non-canonical hydrogen bonds. Due to adjacent electron withdrawing moieties, C-H…O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C-H group. Consequently, the Ca-H groups (adjacent to carbonyl and amino groups of flanking peptide bonds), as well as Ce1-H and Cd2-H groups of histidines (adjacent to imidazole nitrogen atoms) are known to serve as donors in hydrogen bonds, e.g. stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cd1-H group of the indole ring of tryptophan are not well characterized. We perform data mining of high- resolution (r £ 1.5 Å) crystal structures from the Protein Data Bank, and identified ubiquitous close contacts between the Cd1-H groups of tryptophan and a range of electronegative acceptors, specifically main-chain carbonyl oxygen atoms immediately up- and downstream in the polypeptide chain. Our stereochemical analysis shows that most interactions bear all the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum chemical calculations, which reveal energies of the interaction of 1.5–3.0 kcal/mol, depending on the specific stereochemistry. Our study demonstrates that the Cd1-H group of a tryptophan residue plays an important role in stabilizing unique structural motifs by engaging as an H-bond donor with main-chain carbonyl oxygen atoms nearby along the sequence. The most common such interactions involves residues one peptide unit downstream, i.e. i(+1) (Fig 1), or 1–4 peptide units upstream, i.e. i(-1) – i(-4) (Fig. 2). Interestingly, of the possible twelve conformers, Trp is found in these motifs in only six, with the i(+1) class containing only conformers p90, t0, and t-105, while the remaining four classes show Trp only in m105, m0 and p-90. The frequencies of the high-energy m0 and t0 conformers is increased significantly for those classes where the contacts are strongly restricted by short-range steric constraints, while m105, the most populous class found in proteins, is strongly enriched in the i(-3) and i(-4) classes. Our work helps explain the relatively common occurrence of the m0 and t0 classes. It is important to note that the function of Trp residues is intimately contingent on its conformation. For example, Trp in transmembrane helices occurs most often in m0, t0 and p-90 conformations, all of which have been characterized by our study. Of importance is our observation that in the -3 and -4 classes, Trp is often engaged in capping of the acceptor oxygen atom with H-bonds donated by both the amide and Cd1-H groups. We also present evidence based on quantum chemical calculations that the short Cd1-H….O=C contacts revealed by structural data mining are in fact invariably cohesive interactions of the order of approximately half a canonical H-bond, and less sensitive to specific stereochemistry, such as C-H…O and H…O=C angles, then previously thoughts. The critical factor is the position of the hydrogen atom close to the sp2 plane of the acceptor oxygen atom.

Amino Acid Pairing Preferences in Parallel β-Sheets in Proteins

Ab initio restricted Hartree Fock and density functional theory (DFT), as well as semiempirical Austin model 1 and parametrization method 3 molecular orbital calculations were carried out for a range of chlorinated dioxin molecules to obtain molecular descriptors such as HOMO–LUMO gaps (HOMO = highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital) and partial atomic charges. The HOMO–LUMO gap is an indicator of stability in a molecule: the larger the gap the greater the stability of the molecule toward further reaction. These calculations indicate that with increasing extent of chlorination, the gap decreases. The observed charge pattern shows that carbon atoms in the peri (1,4,6,9) ring positions have a partial negative charge while those in the lateral (2,3,7,8) position have a partial positive or small partial negative charge. The descriptors, from the more precise DFT method, were used to rationalize experimental observations of dechlorination of dioxins. Reductive dechlorination pathways from two different experimental studies were examined using partial charges and estimated Gibbs free energy of dechlorination. In both experimental studies, highly thermodynamically favorable and less thermodynamically favorable pathways were observed. For a given chlorinated dioxin, when more than one degradation pathway was possible, dechlorination in the most thermodynamically favored pathway occurred at the most positively charged carbon atom in the ring, which was usually a lateral carbon atom. These results are discussed in light of a possible mechanism for reductive dechlorination.

In order to study the specificities of the contraluminal anion transport systems, the inhibitory potency of substituted benzene analogs on influx of [3H]PAH, [14C]succinate, and [35S]sulfate from the interstitium into cortical tubular cells has been determined in situ: (1) Contraluminal [3H]PAH influx is moderately inhibited by benzene-carboxylate and benzene-sulfonate, and strongly by benzene-dicarboxylates, -disulfonates and carboxy-benzene-sulfonates, if the substituents are located at positions 1 and 3 or 1 and 4. The affinity of the PAH transporter to polysubstituted benzoates increases with increasing hydrophobicity, decreasing electron density at the carboxyl group and decreasing pKa. Similar dependencies are observed for phenols. Benzaldehydes which do not carry an ionic negative charge are accepted by the PAH-transporter, if they possess a second partially charged aldehyde or NO2-group. (2) Contraluminal [14C]succinate influx is inhibited by benzene 1,3- or 1,4-dicarboxylates, -disulfonates and 1,3- or 1,4-carboxybenzene-sulfonates. Monosubstituted benzoates do not interact with the dicarboxylate transporter, but NO2-polysubstituted benzoates do. Phenol itself and 2-substituted phenol interact weakly possibly due to oligomer formation. (3) The contraluminal sulfate transporter interacts only with compounds which show a negative group accumulation such as 3,5-dinitro- or 3,5-dichloro-substituted salicylates. The data are consistent with three separate anion transport systems in the contraluminal membrane: The PAH transporter interacts with hydrophobic molecules carrying one or two negative charges (-COO-, -SO3-) or two or more than two partial negative charges (-OH, -CHO, -SO2NH2, -NO2). The dicarboxylate transporter requires two electronegative ionic charges (-COO-, -SO3-) at 5-9 A distance or one ionic and several partial charges (-Cl, -NO2) at a favourable distance. The sulfate transporter interacts with molecules which have neighbouring electronegative charge accumulation.

In this work, using quantum partial charges, computed from 6-31G(**)B3LYP density functional theory, in molecular dynamics simulations, we found that water inside (6,6) and (10,0) single-walled carbon nanotubes with similar diameters but with different chiralities has remarkably different structural and dynamical properties. Density functional calculations indicate that tubes with different chiralities have significantly different partial charges at the ends of tubes. The partial charges at the ends of a (10,0) tube are around 4.5 times higher than those of a (6,6) tube. Molecular dynamics simulations with the partial charges show different water dipole orientations. In the (10,0) tube, dipole vectors of water molecules at the end of the tube point towards the water reservoir resulting in the formation of an L defect in the center region. This is not observed in the (6,6) tube where dipole vectors of all the water molecules inside the tube point towards either the top or the bottom water reservoir. The water diffusion coefficient is found to increase in the presence of the partial charges. Water in the partially charged (10,0) tube has a lower diffusion coefficient compared to that of in the partially charged (6,6) tube.

A Conserved Negatively Charged Cluster in the Active Site of Creatine Kinase Is Critical for Enzymatic Activity

To assess the estrogenic activity potentially stemming from bisphenol A (BPA) in drinking water, APCI/LC/MS and NMR were used to identify the products of its aqueous chlorination under the following conditions: 500 microg/L bisphenol A and 1.46 mg/L sodium hypochlorite (pH 7.5) at 25 degrees C. The 13 products (4-chloro-BPA; 2,6'-dichloro-BPA; 2,6-dichloro-BPA; 2,2',6'-trichloro-BPA; 2,2',6,6'-tetrachloro-BPA; trichlorophenol; 4-isopropyl-2'-hydroxylphenol; and six kinds of polychlorinated phenoxyphenols (PCPPs)) were found in the chlorinated BPA solution. Three main pathways are proposed: (1) chlorine-substitution reactions on the aromatic ring, followed by dehydration to form the chlorine-substituted BPA, (2) chlorine substitution reactions followed by cleavage of the alpha-C on the isopropyl moiety with positive partial charge and beta'-C on the benzene moiety with a negative partial charge to form trichlorophenol and 4-isopropyl-2'-hydroxylphenol, and (3) the formation of PCPPs. Especially for pathway 2, the reaction mechanism was clarified based on semiempirical quantum mechanical calculations. The reaction proceeded by attack of the OH and Cl (from HOCl) on the alpha-C on the isopropyl moiety with a positive partial charge and on the beta'-C with a negative partial charge on the benzene moiety. The activation energies forthe HOCl/4-chloro-BPA and 2,2',6,6'-tetrachloro-BPA reactions were 0.14 and 0.15 kcal/mol, respectively. Finally, the estrogenic activity of the aqueous chlorinated BPA solution was assessed by an estrogen receptor binding assay and a yeast two-hybrid system. It was found that the binding affinity of the chlorinated aqueous BPA at 60 min was 24 times that before chlorination. The transcriptional activation-induced by products were detected by a yeast two-hybrid system based on the ligand-dependent interaction of two proteins, a human ER and a coactivator, suggesting that the chlorinated BPA solution elicits an ability to mimic the effect of the estrogen hormone.

Molecular Simulations of Nanoscale Transformations in Ionic Semiconductor Nanocrystals

By using Mulliken and Natural Bond Orbital (NBO) methods based on the density functional theory (DFT), partial charges of exocyclic nitrogen atoms were calculated for nitrenium ions formed from 201 known drugs and 50 Ames positive (mutagenic) compounds containing aryl amine and nitro moieties. The statistical difference of the partial charges was analysed based on the hypothesis that the mutagens have a more negative charge on their exocyclic nitrogen atom resulting in stable nitrenium ions, and thus a longer lifetime to react selectively with DNA; whereas known drugs are not in general mutagenic and therefore have a relatively more positive partial charge. The nitrenium ions with 1° amine parent compounds did not show a statistical difference between drugs and mutagens based on the Mulliken charges. A slight difference was observed in the NBO data where the drugs have more negative partial charge on their exocyclic nitrogen atoms compared with the mutagens. Interestingly, nitrenium ions with aryl nitro drugs as their parent compounds have more negative charge on the exocyclic nitrogen compared with the other drug classes. Aryl nitro drugs are relatively scarce and are often linked to genotoxicity, which fits with the hypotheses proposed. These results indicate that other physical properties besides the stability of the nitrenium ions are important to determine the mutagenic potential of aryl amine and nitro containing compounds.

Protein farnesyltransferase is a zinc metalloenzyme that catalyzes the transfer of a 15-carbon farnesyl group to a conserved cysteine residue of a protein substrate. Both electrophilic and nucleophilic mechanisms have been proposed for this enzyme. In this work, we investigate the detailed catalytic mechanism of mammalian protein farnesyltransferase by measuring the effect of metal substitution and/or substrate alterations on the rate constant of the chemical step. Substitution of cadmium for the active site zinc enhances peptide affinity approximately 5-fold and decreases the rate constant for the formation of the thioether product approximately 6-fold, indicating changes in the metal-thiolate coordination in the catalytic transition state. In addition, the observed rate constant for product formation decreases for C3 fluoromethyl farnesyl pyrophosphate substrates, paralleling the number of fluorines at the C3 methyl position and indicating that a rate-contributing transition state has carbocation character. Magnesium ions do not affect the affinity of either the peptide or the isoprenoid substrate but specifically enhance the observed rate constant for product formation 700-fold, suggesting that magnesium coordinates and activates the diphosphate leaving group. These data suggest that FTase catalyzes protein farnesylation by an associative mechanism with an "exploded" transition state where the metal-bound peptide/protein sulfur has a partial negative charge, the C1 of FPP has a partial positive charge, and the bridge oxygen between C1 and the alpha phosphate of FPP has a partial negative charge. This proposed transition state suggests that stabilization of the developing charge on the carbocation and pyrophosphate oxygens is an important catalytic feature.

Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated in silica slit channels filled with 1 M KCl at the point of zero charge by using a hierarchical multiscale simulation methodology. Partial charges of both bulk and surface atoms from ab initio quantum calculations that take into account bond polarization and electronegativity are used in molecular dynamics (MD) simulations to obtain ion and water concentration profiles for channel widths of 1.1, 2.1, 2.75, and 4.1 nm. The interfacial electron density profiles of simulations matched well with that of recent X-ray reflectivity experiments. By simulating corresponding channels with no partial charges, it was observed that the partial charges affect the concentration profiles and transport properties such as diffusion coefficients and mobilities up to a distance of about 3 sigma(O)(-)(O) from the surface. Both in uncharged and partially charged cases, oscillations in concentration profiles of K(+) and Cl(-) ions give rise to an electro-osmotic flow in the presence of an external electric field, indicating the presence of an electric double layer at net zero surface charge, contrary to the expectations from classical continuum theory. I-V curves in a channel-bath system using ionic mobilities from MD simulations were significantly different for channels with and without partial charges for channel widths less than 4.1 nm.

The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.

The structures of two alkylurea inhibitors complexed with murine soluble epoxide hydrolase have been determined by x-ray crystallographic methods. The alkyl substituents of each inhibitor make extensive hydrophobic contacts in the soluble epoxide hydrolase active site, and each urea carbonyl oxygen accepts hydrogen bonds from the phenolic hydroxyl groups of Tyr(381) and Tyr(465). These hydrogen bond interactions suggest that Tyr(381) and/or Tyr(465) are general acid catalysts that facilitate epoxide ring opening in the first step of the hydrolysis reaction; Tyr(465) is highly conserved among all epoxide hydrolases, and Tyr(381) is conserved among the soluble epoxide hydrolases. In one enzyme-inhibitor complex, the urea carbonyl oxygen additionally interacts with Gln(382). If a comparable interaction occurs in catalysis, then Gln(382) may provide electrostatic stabilization of partial negative charge on the epoxide oxygen. The carboxylate side chain of Asp(333) accepts a hydrogen bond from one of the urea NH groups in each enzyme-inhibitor complex. Because Asp(333) is the catalytic nucleophile, its interaction with the partial positive charge on the urea NH group mimics its approach toward the partial positive charge on the electrophilic carbon of an epoxide substrate. Accordingly, alkylurea inhibitors mimic features encountered in the reaction coordinate of epoxide ring opening, and a structure-based mechanism is proposed for leukotoxin epoxide hydrolysis.