The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals

We have studied the thermodynamic properties of hen egg white lysozyme crystals using a novel simulation method combining atomistic Monte Carlo simulation to calculate van der Waals interactions and the boundary element method to solve the Poisson-Boltzmann equation for the electrostatic interactions. For computational simplicity, we treat the protein as a rigid body, using the crystallographic coordinates of all non-hydrogen atoms of the protein to describe the detailed shape. NVT Monte Carlo simulations are carried out for tetragonal and orthorhombic crystals to obtain the van der Waals energy, incorporating an implicit solvation effect. For crystal phases, an optimally linearized Poisson-Boltzmann equation is used to include the effect of the Donnan equilibrium of the salt ions. The Helmholtz energy is obtained from expanded ensemble Monte Carlo simulations. By using the force field parameters that had previously been tuned for the solution properties, reasonable agreement with experiment is found for the crystallization energy of the tetragonal form. The prediction of the entropy is also reasonable with a slight underestimation suggesting the release of a few water molecules per protein during the crystallization. However, the predictions of the properties of the orthorhombic crystal are poor, probably due to differences in the solvation structure as indicated by experiments, and also as a result of the approximate force field used.     

Measurement of mobility of adsorbed colloids by lateral force microscopy

The surface mobility of colloidal latex particles adsorbed on mica was measured by moving the particles with an AFM tip in the lateral force microscopy mode. The same particle was repeatedly scanned while the normal force was gradually increased, until the particle was displaced from its location on the substrate. The lateral (friction) force curve obtained for that scan was then used to determine the force needed to displace the particle. The data accumulated for approximately 100 particles indicate a wide distribution in the lateral force required. However, the data show that the mean lateral force is proportional to the particle diameter, with the effect of electrostatic interactions on the mobility of adsorbed particles seen to be weak. These results are consistent with classical theories of friction in macroscopic systems.     

Casein precipitation equilibria in the presence of calcium ions and phosphates

Calcium ion induced aggregation and precipitation equilibria of β-casein were studied in the presence or absence of mono- and polyphosphates at pH 5.5 and 7.5. We analyze the data by assuming ion binding at a well-defined stoichiometric ratio, leading to protein charge neutralization and formation of slightly soluble complexes. The precipitation curves are in good agreement with the model, showing the expected larger induction region and steeper slope at the lower pH. The addition of phosphates leads to better precipitation of the protein, which can be explained by a mechanism involving the formation of calcium phosphate microcrystals. These crystals provide a substrate for protein adsorption, with subsequent cross-binding of the casein micelles and formation of sturdy aggregates of co-precipitated calcium phosphate and casein. The crystallite formation leads to effective separations in commercial caseinates, which would be impossible with Ca²⁺ alone.     

Causal loop diagrams as a de-escalation technique

Escalation of commitment, the tendency of decision makers to keep on investing in losing courses of action, has been shown to be a costly decision bias that affects many areas of decision making. Even though escalation is a widely studied phenomenon, there has been comparatively little research on how to avoid this bias. The present study focuses on de-escalation of commitment and proposes that causal loop diagrams (CLDs) can help to decrease escalating commitment to a failing course of action. By means of an experiment, this study shows that using a CLD decreases escalation tendencies.     

Effects of pore structure and molecular size on diffusion in chromatographic adsorbents

Two computational approaches, namely Brownian dynamics and network modeling, are presented for predicting effective diffusion coefficients of probes of different sizes in three chromatographic adsorbents, the structural properties of which were determined previously using electron tomography. Three-dimensional reconstructions of the adsorbents provide detailed, explicit characteristics of the pore network, so that no assumptions have to be made regarding pore properties such as connectivity, pore radius and pore length. The diffusivity predictions obtained from the two modeling approaches were compared to experimental diffusivities measured for dextran and protein probes. Both computational methods captured the same qualitative results, while their predictive capabilities varied among adsorbents.     

Biotinyl-Glucose-6-Phosphate Dehydrogenase Preparation,Kinetics, and Modulation by Avidin

The kinetics of free glucose-6-phosphate dehydrogenase (G-6-PDH), biotinylated G-6-PDH, and biotinylated G-6-PDH complexed with avidin were investigated. The kinetics of the free enzyme were consistent with a sequential rather than a ping-pong mechanism. The kinetics of the biotinylated enzyme were similar to that of the free enzyme, but the kinetic constants were different; theK _m value for NADP was halved, whereas theK _m for G-6-P decreased only slightly. In the presence of avidin, theK _m of biotinylated G-6-PDH for G-6-P nearly doubled whereas theK _m for NADP did not change significantly. Avidin complexed with biotinylated G-6-PDH inhibited the enzyme from acting. Based upon these reactions, it was possible to devise assays for either free biotin or free avidin using biotinylated G-6-PDH as the indicator enzyme. Concentrations of biotin between 40 and 60 mg/mL, or of 25–95 Μg/mL of avidin could be measured within 2 min through the use of biotinylated G-6-PDH.     

Synthesis and Diels-Alder Reactions of a New Kind of Chiral Dienophiles: Cyclic Vinyl-p-tolylsulfilimines

A new kind of chiral dienophiles, cyclic vinyl-p-tolylsulfilimines (2a and 2b), were obtained from the corresponding (Z)-sulfinylacrylonitriles with HBF(4) and methanol. The asymmetric Diels-Alder reaction of optically pure 2a with cyclopentadiene under mild thermal or catalyzed conditions afforded only the endo-4a adduct with complete endo and pi-facial selectivities. The ability of the sulfilimine moiety to enhance the dienophilic reactivity of the double bond is similar to that of the sulfinyl group.     

Separation-free amperometric enzyme immunoassay

A new technique for conducting a separation-free amperometric enzyme immunoassay is described using DNP-aminocaproic acid as the analyte. The technique is based on the combined use of a recently described separation-free enzyme immunoassay (19) and an electrode system that senses H₂O₂. Oxidation of glucose to gluconate and H₂O₂ by the enzyme reconstituted from DNP-conjugate apoglucose oxidase (DPN-CAGO) and FAD was continuously measured amperometrically. The reconstitution was inhibited by preincubation with anti-DNP antibody before adding FAD. This antibody-induced inhibition of the reconstituting of the holoenzyme was reversed by adding DNP-amino caproic acid to DNP-CAGO before adding the antibody to DNP-CAGO. Based on (a) the antibody-induced inhibition of holoenzyme reconstitution, (b) a specific ligand-induced reversal of the inhibition, and (c) an electrochemical system that measures H₂O₂, we developed a separation-free (homogeneous) amperometric enzyme immunoassay.