Experimental intensity patterns obtained from a 2D shearing interferometer with adaptable sensitivity

The interferometric intensity patterns from a 2D shearing interferometer are shown and discussed. The intensity patterns can be obtained in two different approaches incorporating differential and extended wavefront controlled displacements. The reliable directional sensitivity of this interferometer allows the optimization of the measurement parameters to estimate the wavefront of the intensity patterns by regularization techniques.     

Effects of tributyltin(IV) chloride on the gametes and fertilization of Ascidia malaca (Ascidiacea: Tunicata)

Ascidia malaca gametes before fertilization incubated in 10^?5 or 10^?7 M solutions of tributyltin(IV) chloride, TBTCl, for 3 h appear highly damaged under transmission electron microscopy observation. Also, the fertilization process is affected by the compound: the damaged spermatozoa are present in the vitelline coat and the egg does not cleave. An increase of microbodies, structurally similar to peroxisomes, have been detected in the egg peripheral cytoplasm, probably in relation to their role in alleviating damage to some cellular components. The results have shown that the reproduction of ascidians under unfavourable environmental conditions is prevented. Copyright © 2003 John Wiley & Sons, Ltd.     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Variational transition state theory without the minimum-energy path

In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions OH+H₂→H₂O+H and C₂H₅→C₂H₄+H are very encouraging. Received: 22 January 1997 / Accepted: 11 March 1997