Site directed mutagenesis at position 193 of human trypsin 4 alters the rate of conformational change during activation: Role of local internal viscosity in protein dynamics

An evolving view on food viscosity regulating gastric emptying

Viscosity is a property of most foods. The consumption of the high-viscosity food is associated with a variety of physiological responses, one of which is their ability to regulate gastric emptying and modulate postprandial glycemic response. Gastric emptying has been proven to be a key step affecting the digestion and absorption of food, whereas, the relationship between viscosity and gastric emptying is still far away from being understood. Here, we reviewed the factors that influence food viscosity and food viscosity changes during digestion. Besides, the effect of food viscosity on gastric emptying and food-viscosity-physiological response were highlighted. Finally, "quantitative relationship" of viscosity and gastric emptying was discussed. This review can contribute to the understanding that how food viscosity affects gastric emptying, and help for developing foods that could control satiety and manage body weight for the specific populations.

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

Effect of ethanol, glycerol, glucose and tartaric acid on the viscosity of model aqueous solutions and wine samples

Viscosity is a property that exerts great influence on the body of wines, since it affects the sensation of thickness in the mouth. The present study refers to the quantitative correlation of the major components of wine, alcohol, reduced sugar, glycerol and total acidity, in its viscosity. Various model aqueous solutions consisting of these components were prepared and viscosity was measured at 20 °C. Each component was studied either alone or in mixtures with the others. Viscosity of white dry wines samples was also measured. From the experimental results, linear multi-dependence equations were derived, which correlate the viscosity with the concentration of the components of the solutions, each of them alone and in combination. Glucose was found to affect viscosity of model aqueous solutions the most, whereas ethanol had the least effect. The knowledge of these factors may have a practical value in optimizing wine's body.

Internal friction in enzyme reactions

The empirical concept of internal friction was introduced 20 years ago. This review summarizes the results of experimental and theoretical studies that help to uncover the nature of internal friction. After the history of the concept, we describe the experimental challenges in measuring and interpreting internal friction based on the viscosity dependence of enzyme reactions. We also present speculations about the structural background of this viscosity dependence. Finally, some models about the relationship between the energy landscape and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions are also discussed.

Temperature dependence of internal friction in enzyme reactions

Our aim was to elucidate the physical background of internal friction of enzyme reactions by investigating the temperature dependence of internal viscosity. By rapid transient kinetic methods, we directly measured the rate constant of trypsin 4 activation, which is an interdomain conformational rearrangement, as a function of temperature and solvent viscosity. We found that the apparent internal viscosity shows an Arrhenius-like temperature dependence, which can be characterized by the activation energy of internal friction. Glycine and alanine mutations were introduced at a single position of the hinge of the interdomain region to evaluate how the flexibility of the hinge affects internal friction. We found that the apparent activation energies of the conformational change and the internal friction are interconvertible parameters depending on the protein flexibility. The more flexible a protein was, the greater proportion of the total activation energy of the reaction was observed as the apparent activation energy of internal friction. Based on the coupling of the internal and external movements of the protein during its conformational change, we constructed a model that quantitatively relates activation energy, internal friction, and protein flexibility.