A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation

In 2004, we used NMR to solve the structure of the minor groove binder thiazotropsin A bound in a 2 : 1 complex to the DNA duplex, d(CGACTAGTCG)2. In this current work, we have combined theory and experiment to confirm the binding thermodynamics of this system. Molecular dynamics simulations that use polarizable or non-polarizable force fields with single and separate trajectory approaches have been used to explore complexation at the molecular level. We have shown that the binding process invokes large conformational changes in both the receptor and ligand, which is reflected by large adaptation energies. This is compensated for by the net binding free energy, which is enthalpy driven and entropically opposed. Such a conformational change upon binding directly impacts on how the process must be simulated in order to yield accurate results. Our MM-PBSA binding calculations from snapshots obtained from MD simulations of the polarizable force field using separate trajectories yield an absolute binding free energy (-15.4 kcal mol-1) very close to that determined by isothermal titration calorimetry (-10.2 kcal mol-1). Analysis of the major energy components reveals that favorable non-bonded van der Waals and electrostatic interactions contribute predominantly to the enthalpy term, whilst the unfavorable entropy appears to be driven by stabilization of the complex and the associated loss of conformational freedom. Our results have led to a deeper understanding of the nature of side-by-side minor groove ligand binding, which has significant implications for structure-based ligand development

Monitoring the bioactive compounds in culinary transformation of soymilk : an in situ quantitative NMR study.

Many products made from soybean are consumed in Asia. Soymilk, tofu and yuba are obtained by individuals at home. Changes of bioactive compounds during culinary process were rarely reported. In this study, the analytical method called “in situ quantitative nuclear magnetic resonance spectroscopy” (isq 1H NMR) was applied to the quantitative determination of the variation in taste and functional molecules that are sucrose, lysine, arginine and valine during various culinary transformations of soymilk, involving fresh, thermal process, vacuum evaporation, tofu and yuba. Results suggest that thermal process at 100 ̊C increased the amount of free sucrose but significantly decreased the amount of lysine. Sweetness of soymilk could be simply enhanced. Evaporation of soymilk caused a higher reduction of lysine than thermal processing at 100 °C, indicating that complexation and Maillard reactions of lysine could be enhanced. The arginine content also decreased, albeit in less quantities. The changes of molecular conformation could also be monitored. In particular, resonances associated with the side-chain of valine were observed when most proteins were unfolded at high temperature. In mild acidic condition using glucono-delta-lactone as a coagulant, the amount of lysine was maintained higher than thermal process and evaporation while sucrose content was reduced. Tofu containing of lysine and sucrose could have a sweetness taste. However, there was no free sucrose in yuba. Understanding the change of taste molecules in soymilk during culinary transformation could lead to a better formulate soymilk products, thus this would be benefit to culinary application at home and industrial

Characteristic vibration patterns of odor compounds from bread-baking volatiles upon protein binding : density functional and ONIOM study and principal component analysis

As the mechanism underlying the sense of smell is unclear, different models have been used to rationalize structure–odor relationships. To gain insight into odorant molecules from bread baking, binding energies and vibration spectra in the gas phase and in the protein environment [7-transmembrane helices (7TMHs) of rhodopsin] were calculated using density functional theory [B3LYP/6-311++G(d,p)] and ONIOM [B3LYP/6-311++G(d,p):PM3] methods. It was found that acetaldehyde (“acid” category) binds strongly in the large cavity inside the receptor, whereas 2-ethyl-3-methylpyrazine (“roasted”) binds weakly. Lys296, Tyr268, Thr118 and Ala117 were identified as key residues in the binding site. More emphasis was placed on how vibrational frequencies are shifted and intensities modified in the receptor protein environment. Principal component analysis (PCA) suggested that the frequency shifts of C–C stretching, CH3 umbrella, C = O stretching and CH3 stretching modes have a significant effect on odor quality. In fact, the frequency shifts of the C–C stretching and C = O stretching modes, as well as CH3 umbrella and CH3 symmetric stretching modes, exhibit different behaviors in the PCA loadings plot. A large frequency shift in the CH3 symmetric stretching mode is associated with the sweet-roasted odor category and separates this from the acid odor category. A large frequency shift of the C–C stretching mode describes the roasted and oily-popcorn odor categories, and separates these from the buttery and acid odor categories

Effect of the Addition of Soybean Residue (Okara) on the Physicochemical, Tribological, Instrumental, and Sensory Texture Properties of Extruded Snacks

An extrusion process was used to improve the physical and textural characteristics of an extruded snack supplemented with soybean residue (okara). An extreme vertices mixture design with a constraint for okara flour (0–50%), mung bean flour (20–70%), and rice flour (20–80%) resulted in the production of eleven formulations. The color, radial expansion index (REI), bulk density, tribological behavior, and instrumental and sensory texture of the extruded snacks were evaluated. Increasing the quantity of okara resulted in an extrudate with a darker, redder color, decreased REI, increased bulk density, and decreased crispness. The tribological pattern of the snack was determined by its dominant composition (protein, starch, or fiber) in the flour mixture, which contributed to the stability of the lubricating film under rotational shear. A principal component analysis of sensory data captured a total of 81.9% variations in the first two dimensions. Texture appeal was inversely related to tooth packing (r = −0.646, p < 0.05). The optimized formulation for texture preference had an okara content of 19%, which was 104% crispier and 168% tougher than an okara content of 40%. This by-product of soybean milk processing can thus be used to develop gluten-free snacks with desirable physical characteristics and texture