The Influence of Amino Acid Protonation States on Molecular Dynamics Simulations of the Bacterial Porin OmpF

Several groups, including our own, have found molecular dynamics (MD) calculations to result in the size of the pore of an outer membrane bacterial porin, OmpF, to be reduced relative to its size in the x-ray crystal structure. At the narrowest portion of its pore, loop L3 was found to move toward the opposite face of the pore, resulting in decreasing the cross-section area by a factor of ∼2. In an earlier work, we computed the protonation states of titratable residues for this system and obtained values different from those that had been used in previous MD simulations. Here, we show that MD simulations carried out with these recently computed protonation states accurately reproduce the cross-sectional area profile of the channel lumen in agreement with the x-ray structure. Our calculations include the investigation of the effect of assigning different protonation states to the one residue, D(127), whose protonation state could not be modeled in our earlier calculation. We found that both assumptions of charge states for D(127) reproduced the lumen size profile of the x-ray structure. We also found that the charged state of D(127) had a higher degree of hydration and it induced greater mobility of polar side chains in its vicinity, indicating that the apparent polarizability of the D(127) microenvironment is a function of the D(127) protonation state

Theology, Politics and Society: the Missing Link. Studying Religion in the Mamluk Period

The chapter focuses on a few problematic topics which have so far received little attention in contemporary scholarship on religion in the Mamluk period. In particular it tries to shed light on what the author describes as a missing link between theological production and its social and political significance, between theologians and society at large, between ideas about God and their relevance to people\u2019s lives. The article argues that exploring the link between society and theology may be a rewarding research enterprise. An attention to this link is generally missing in scholarship both on the intellectual and the socio-religious history of the Mamluk period. The paper identifies the reasons for this state of affairs and provides a sample of materials that proves that we do not lack the resources for pursuing research in this direction. The paper advocates an interdisciplinary approach where the efforts of experts in Islamic theology and historians interested in religion and society ought to merge