Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors.

While relative binding free energy (RBFE) calculations using alchemical methods are routinely carried out for many pharmaceutically relevant protein targets, challenges remain. For example, open-source tools do not support the easy setup and simulation of metalloproteins, particularly when ligands directly coordinate to the metal site. Here, we evaluate the performance of RBFE methods for KPC-2, a serine-β-lactamase (SBL), and two nonbonded metal parameter setups for VIM-2, a metallo-β-lactamase (MBL) with two active site zinc ions.

Human DNA from the oldest Eneolithic cemetery in Nalchik points the spread of farming from the Caucasus to the Eastern European steppes.

The Darkveti-Meshoko culture (c.5000-3500/3300 BCE) is the earliest known farming community in the Northern Caucasus, but its contribution to the genetic profile of the neighboring steppe herders has remained unclear. We present analysis of human DNA from the Nalchik cemetery-the oldest Eneolithic site in the Northern Caucasus-which shows a link with the LowerVolga's first herders of the Khvalynsk culture.

CsrA controls ToxR levels by increasing the stability and translation of mRNA.

Intestinal colonization and virulence factor production in response to environmental cues is mediated through several regulatory factors in , including the highly conserved RNA-binding global regulatory protein CsrA. We have shown previously that CsrA increases synthesis of the virulence-associated transcription factor ToxR in response to specific amino acids (NRES) and is required for the virulence of in the infant mouse model of cholera. In this study, we mapped the 5' untranslated region (5' UTR) of and showed that CsrA can bind directly to an RNA sequence encompassing the 5' UTR, indicating that the regulation of ToxR levels by CsrA is direct.

Comparison of Methodologies for Absolute Binding Free Energy Calculations of Ligands to Intrinsically Disordered Proteins.

Modulating the function of Intrinsically Disordered Proteins (IDPs) with small molecules is of considerable importance given the crucial roles of IDPs in the pathophysiology of numerous diseases. Reported binding affinities for ligands to diverse IDPs vary broadly, and little is known about the detailed molecular mechanisms that underpin ligand efficacy. Molecular simulations of IDP ligand binding mechanisms can help us understand the mode of action of small molecule inhibitors of IDP function, but it is still unclear how binding energies can be modeled rigorously for such a flexible class of proteins.

CsrA controls ToxR levels by increasing the stability and translation of mRNA.

Unlabelled: Regulation of colonization and virulence factor production in response to environmental cues is mediated through several regulatory factors in , including the highly conserved RNA-binding global regulatory protein CsrA. We have shown previously that CsrA increases synthesis of the virulence-associated transcription factor ToxR in response to specific amino acids (NRES) and is required for the virulence of in the infant mouse model of cholera. In this study, we mapped the 5' untranslated region (5' UTR) of and showed that CsrA can bind directly to an RNA sequence encompassing the 5' UTR, indicating that the regulation of ToxR levels by CsrA is direct.