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181.
Aromatic residues play a key role in saccharide-binding sites. Experimental studies have given an estimate of the energetics of saccharide-aromatic residue interactions. In this study, dependence of the energetics on the mutual position-orientation (PO) of saccharide and aromatic residue has been investigated by geometry optimization of a very large number (164) of complexes at MP2/6-31G(d,p) level of theory. The complexes are of Tyr and Phe analogs with α/β-D-Glc, β-D-Gal, α-D-Man and α/β-L-Fuc. A number of iso-energy POs are found for the complexes of all six saccharides. Stacking and non-stacking modes of binding are found to be of comparable strengths. In general, complexes of p-OHTol are stronger than those of Tol, and those dominated by OH···O interactions are more stable than ones dominated by CH···π interactions. The strengths of OH···O/π interactions, but not those of CH···π, show large variations. Even though an aromatic residue has a large variety of POs to interact with a saccharide, distinct preferences are found due to anomeric and epimeric differences. An aromatic residue can interact from either the a- or b-face of Glc, but only through the b-face with Gal, its C4-epimer. In contrast, stacking interaction with Man (C2-epimer of Glc) requires the participation of the -CH(2)OH group and free rotation of this group, as is observed in solution, precludes all modes of stacking interactions. It is also found that an aromatic residue can be strategically placed either to discriminate or to accommodate (i) anomers of Glc and of Fuc and (ii) Gal/Fuc. Thus, analysis of the optimized geometries of by far the largest number of complexes, and with six different saccharides, at this level of theory has given insights into how Nature cleverly uses aromatic residues to fine tune saccharide specificities of proteins. These are of immense utility for protein engineering and protein design studies. 相似文献
182.
We consider the numerical approximation of a singularly perturbed time delayed convection diffusion problem on a rectangular domain. Assuming that the coefficients of the differential equation be smooth, we construct and analyze a higher order accurate finite difference method that converges uniformly with respect to the singular perturbation parameter. The method presented is a combination of the central difference spatial discretization on a Shishkin mesh and a weighted difference time discretization on a uniform mesh. A?priori explicit bounds on the solution of the problem are established. These bounds on the solution and its derivatives are obtained using a suitable decomposition of the solution into regular and layer components. It is shown that the proposed method is $L_{2}^{h}$ -stable. The analysis done permits its extension to the case of adaptive meshes which may be used to improve the solution. Numerical examples are presented to demonstrate the effectiveness of the method. The convergence obtained in practical satisfies the theoretical predictions. 相似文献
183.
Nikhil Taxak Prashant V. Desai Bhargav Patel Michael Mohutsky Valentine J. Klimkowski Vijay Gombar Prasad V. Bharatam 《Journal of computational chemistry》2012,33(21):1740-1747
Mechanism‐based inhibition (MBI) of cytochrome P450 (CYP) can lead to drug–drug interactions and often to toxicity. Some aliphatic and aromatic amines can undergo biotransformation reactions to form reactive metabolites such as nitrosoalkanes, leading to MBI of CYPs. It has been proposed that the nitrosoalkanes coordinate with the heme iron, forming metabolic‐intermediate complex (MIC), resulting in the quasi‐irreversible inhibition of CYPs. Limited mechanistic details regarding the formation of reactive nitroso intermediate and its coordination with heme‐iron have been reported. A quantum chemical analysis was performed to elucidate potential reaction pathways for the generation of nitroso intermediate and the formation of MIC. Elucidation of the energy profile along the reaction path, identification of three‐dimensional structures of reactive intermediates and transition states, as well as charge and spin density analyses, were performed using the density functional B3LYP method. The study was performed using Cpd I [iron (IV‐oxo] heme porphine with SH? as the axial ligand) to represent the catalytic domain of CYP, simulating the biotransformation process. Three pathways: (i) N‐oxidation followed by proton shuttle, (ii) N‐oxidation followed by 1,2‐H shift, and (iii) H‐abstraction followed by rebound mechanism, were studied. It was observed that the proton shuttle pathway was more favorable over the whole reaction leading to reactive nitroso intermediate. This study revealed that the MIC formation from a primary amine is a favorable exothermic process, involving eight different steps and preferably takes place on the doublet spin surface of Cpd I . The rate‐determining step was identified to be the first N‐oxidation of primary amine. © 2012 Wiley Periodicals, Inc. 相似文献
184.
Einstein and others derived the reciprocal dependence of the self-diffusivity D on the solute radius r(u) for large solutes based on kinetic theory. We examine here (a) the range of r(u) over which Stokes-Einstein (SE) dependence is valid and (b) the precise dependence for small solutes outside of the SE regime. We show through molecular dynamics simulations that there are two distinct regimes for smaller solutes: (i) the interaction or Levitation effect (LE) regime for solutes of intermediate size and (ii) the D proportional, variant 1/r(u)(2) for still smaller solutes. We show that as the solute-solvent size ratio decreases, the breakdown in the Stokes-Einstein relationship leading to the LE regime has its origin in dispersion interaction between the solute and the solvent. These results explain reports of enhanced solute diffusion in solvents existing in the literature seen for small solutes for which no explanation exists. 相似文献
185.
Mukherjee S Bansal M Bhattacharyya D 《Journal of computer-aided molecular design》2006,20(10-11):629-645
Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA. 相似文献
186.
Bidisha Borkakaty Kanwar Sen Manju Agarwal 《Mathematical and Computer Modelling》2009,50(7-8):1067-1082
In this paper, we find the busy period density of queues in explicit computational form, through lattice path (LP) approach. Both the arrival and service time distributions are approximated by 2-phase Cox distribution C2, which has a Markovian property enabling us to use LP combinatorics. Since any distribution with rational Laplace–Stieltjes transform (LST) and square coefficient of variation (CV2) lying in [1/2,∞) can be approximated by a C2([M. Agarwal, K. Sen, B. Borkakaty, Busy period density of queueing system C3/M/1, Journal of Combinatorics, Information and Systems Sciences 31 (1–4) (2006) 127–161]), the results obtained would be applicable to a very wide class of distributions occurring in real life. 相似文献
187.
Manju Rajeswaran Thomas N. Blanton Ralph H. Young William Brennessel 《Journal of chemical crystallography》2010,40(3):195-200