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The ability to discriminate cell adhesion molecule expression between healthy and inflamed endothelium is critical for therapeutic intervention in many diseases. This study explores the effect of laminar flow on TNFα-induced E-selectin surface expression levels in human umbilical vein endothelial cells (HUVECs) relative to IL-1β-induced expression via flow chamber assays. HUVECs grown in static culture were either directly (naïve) activated with cytokine in the presence of laminar shear or pre-exposed to 12 h of laminar shear (shear-conditioned) prior to simultaneous shear and cytokine activation. Naïve cells activated with cytokine in static served as control. Depending on the cell shear history, fluid shear is found to differently affect TNFα-induced relative to IL-1β-induced HUVEC expression of E-selectin. Specifically, E-selectin surface expression by naïve HUVECs is enhanced in the 8-12 h activation time range with simultaneous exposure to shear and TNFα (shear-TNFα) relative to TNFα static control whereas enhanced E-selectin expression is observed in the 4-24 h range for shear-IL-1β treatment relative to IL-1β static control. While exposure of HUVECs to shear preconditioning mutes shear-TNFα-induced E-selectin expression, it enhances or down-regulates shear-IL-1β-induced expression dependent on the activation period. Under dual-cytokine-shear conditions, IL-1β signaling dominates. Overall, a better understanding of E-selectin expression pattern by human ECs relative to the combined interaction of cytokines, shear profile and history can help elucidate many disease pathologies., (Copyright © 2012 Wiley Periodicals, Inc.)

Cation-π interaction is comparable and as important as other main molecular interaction types, such as hydrogen bond, electrostatic interaction, van der Waals interaction, and hydrophobic interaction. Cation-π interactions frequently occur in protein structures, because six (Phe, Tyr, Trp, Arg, Lys, and His) of 20 natural amino acids and all metallic cations could be involved in cation-π interaction. Cation-π interactions arise from complex physicochemical nature and possess unique interaction behaviors, which cannot be modeled and evaluated by existing empirical equations and force field parameters that are widely used in the molecular dynamics. In this study, the authors present an empirical approach for cation-π interaction energy calculations in protein interactions. The accurate cation-π interaction energies of aromatic amino acids (Phe, Tyr, and Try) with protonated amino acids (Arg and Lys) and metallic cations (Li(+), Na(+), K(+), and Ca(2+)) are calculated using B3LYP/6-311+G(d,p) method as the benchmark for the empirical formulization and parameterization. Then, the empirical equations are built and the parameters are optimized based on the benchmark calculations. The cation-π interactions are distance and orientation dependent. Correspondingly, the empirical equations of cation-π interactions are functions of two variables, the distance r and the orientation angle θ. Two types of empirical equations of cation-π interactions are proposed. One is a modified distance and orientation dependent Lennard-Jones equation. The second is a polynomial function of two variables r and θ. The amino acid-based empirical equations and parameters provide simple and useful tools for evaluations of cation-π interaction energies in protein interactions., (Copyright © 2011 Wiley Periodicals, Inc.)

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus., ((c) 2008 Wiley Periodicals, Inc.)

Most embryonic stem (ES) cell research is performed with a gas phase oxygen partial pressure (pO(2)) of 142 mmHg, whereas embryonic cells in early development are exposed to pO(2) values of 0-30 mmHg. To understand effects of these differences, we studied murine ES (mES) growth, maintenance of stem cell phenotype, and cell energetics over a pO(2) range of 0-285 mmHg, in the presence or absence of differentiation-suppressing leukemia inhibitory factor (LIF). With LIF, growth rate was sensitive to pO(2) but constant with time, and expression of self-renewal transcription factors decreased at extremes of pO(2). Subtle morphological changes suggested some early differentiation, but cells retained the ability to differentiate into derivatives of all three germ layers at low pO(2). Without LIF, growth rate decreased with time, and self-renewal transcription factor mRNA decreased further. Gross morphological changes occurred, and overt differentiation occurred at all pO(2). These findings suggested that hypoxia in the presence of LIF promoted limited early differentiation. ES cells survived oxygen starvation with negligible cell death by increasing anaerobic metabolism within 48 h of anoxic exposure. Decreasing pO(2) to 36 mmHg or lower decreased oxygen consumption rate and increased lactate production rate. The fraction of ATP generated aerobically was 60% at or above 142 mmHg and decreased to 0% under anoxia, but the total ATP production rate remained nearly constant at all pO(2). In conclusion, undifferentiated ES cells adapt their energy metabolism to proliferate at all pO(2) between 0 and 285 mmHg. Oxygen has minimal effects on undifferentiated cell growth and phenotype, but may exert more substantial effects under differentiating conditions.

A new drug design method, the multiple field three-dimensional quantitative structure-activity relationship (MF-3D-QSAR), is proposed. It is a combination and development of classical 2D-QSAR and traditional 3D-QSAR. In addition to the electrostatic and van der Waals potentials, more potential fields (such as lipophilic potential, hydrogen bonding potential, and nonthermodynamic factors) are integrated in the MF-3D-QSAR. Meanwhile, a principal component analysis (PCA) and iterative double least square (IDLS) technique is developed for predicting the bioactivity of query drug candidates. As an example, the MF-3D-QSAR is applied to the design of neuraminidase inhibitor and to prove its predictive power, and some useful findings are obtained for developing drugs against influenza virus., ((c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2008.)

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so-called AABPD (amino acid based-peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three-dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three-dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C-like proteinase and the affinity prediction for epitope-peptides with Class I MHC molecules are studied by using the peptide reagent design strategy., (Copyright 2007 Wiley Periodicals, Inc.)

A novel method has been developed for the separation of bioproducts from yeast cells. The method uses a combination of physical, chemical, and biological agents such as lytic enzymes, osmotic supports, and spheroplast stabilizers. Using this technique, products (proteins and enzymes) can be released from specific cell locations at different process states; it has thus been celled differential product release (DPR). The wall-associated proteins are released first and the lytic enzyme is removed together with the wall proteins at this stage. Secondly, the cytosol products are released by a mild procedure during which the organelles remained intact. Finally, the organelle proteins are solubilized. In each stage, specific proteins are released while others are kept inside the different cell compartments. This method can be used with relatively high yeast concentrations (up to 145 g dry wt/L) and gives higher product recoveries and much higher selectivity than mechanical disruption.