Publications by Year: 1997

Raychaudhuri S, Younas F, Karplus PA, Faerman CH, Ripoll DR. Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins [Internet]. Protein Sci 1997;6(9):1849-57. Publisher's VersionAbstract
The electrostatic properties of seven alpha/beta-barrel enzymes selected from different evolutionary families were studied: triose phosphate isomerase, fructose-1,6-bisphosphate aldolase, pyruvate kinase, mandelate racemase, trimethylamine dehydrogenase, glycolate oxidase, and narbonin, a protein without any known enzymatic activity. The backbone of the alpha/beta-barrel has a distinct electrostatic field pattern, which is dipolar along the barrel axis. When the side chains are included in the calculations the general effect is to modulate the electrostatic pattern so that the electrostatic field is generally enhanced and is focused into a specific area near the active site. We use the electrostatic flux through a square surface near the active site to gauge the functionally relevant magnitude of the electrostatic field. The calculations reveal that in six out of the seven cases the backbone itself contributes greater than 45% of the total flux. The substantial electrostatic contribution of the backbone correlates with the known preference of alpha/beta-barrel enzymes for negatively charged substrates.
Van Liew HD, Raychaudhuri S. Stabilized bubbles in the body: pressure-radius relationships and the limits to stabilization [Internet]. J Appl Physiol (1985) 1997;82(6):2045-53. Publisher's VersionAbstract
We previously outlined the fundamental principles that govern behavior of stabilized bubbles, such as the microbubbles being put forward as ultrasound contrast agents. Our present goals are to develop the idea that there are limits to the stabilization and to provide a conceptual framework for comparison of bubbles stabilized by different mechanisms. Gases diffuse in or out of stabilized bubbles in a limited and reversible manner in response to changes in the environment, but strong growth influences will cause the bubbles to cross a threshold into uncontrolled growth. Also, bubbles stabilized by mechanical structures will be destroyed if outside influences bring them below a critical small size. The in vivo behavior of different kinds of stabilized bubbles can be compared by using plots of bubble radius as a function of forces that affect diffusion of gases in or out of the bubble. The two ends of the plot are the limits for unstabilized growth and destruction; these and the curve's slope predict the bubble's practical usefulness for ultrasonic imaging or O2 carriage to tissues.