The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.Comment: Revised manuscrip

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

The aerotolerant anaerobe Streptococcus pneumoniae is part of the normal nasopharyngeal microbiota of humans and one of the most important invasive pathogens. A genomic survey allowed establishing the occurrence of twenty-one phosphotransferase systems, seven carbohydrate uptake ABC transporters, one sodium∶solute symporter and a permease, underlining an exceptionally high capacity for uptake of carbohydrate substrates. Despite high genomic variability, combined phenotypic and genomic analysis of twenty sequenced strains did assign the substrate specificity only to two uptake systems. Systematic analysis of mutants for most carbohydrate transporters enabled us to assign a phenotype and substrate specificity to twenty-three transport systems. For five putative transporters for galactose, pentoses, ribonucleosides and sulphated glycans activity was inferred, but not experimentally confirmed and only one transport system remains with an unknown substrate and lack of any functional annotation. Using a metabolic approach, 80% of the thirty-two fermentable carbon substrates were assigned to the corresponding transporter. The complexity and robustness of sugar uptake is underlined by the finding that many transporters have multiple substrates, and many sugars are transported by more than one system. The present work permits to draw a functional map of the complete arsenal of carbohydrate utilisation proteins of pneumococci, allows re-annotation of genomic data and might serve as a reference for related species. These data provide tools for specific investigation of the roles of the different carbon substrates on pneumococcal physiology in the host during carriage and invasive infection

Structural characterization of agmatine at physiological conditions

Abstract The present work aims at determining the structure–activity relationships (SAR’s) which rule the biological function of agmatine (4-(aminobutyl)guanidinium, AGM), a biogenic amine produced by decarboxylation of arginine. Its structural preferences, both as an isolated molecule and in aqueous solution (namely at physiological conditions) were ascertained, by vibrational (Raman) spectroscopy coupled to theoretical (density functional) calculations. An evaluation of mitochondrial functions (membrane potential (??), mitochondrial swelling, and cytochrome c release) in rat liver mitochondria (RLM) was also carried out. The results thus obtained, coupled to the conformational analysis performed for the distinct polyamine protonation states, allowed to individualize the agmatine structures which interact with the mitochondrial site responsible for its transport and for the protection against mitochondrial permeability transition (MPT) induction, as well as to gain information on the specific mechanisms involved

Spectroscopic and electrochemical studies of cocaine–opioid interactions

Abstract The drugs of abuse cocaine (C), heroin (H), and morphine (M) have been studied to enable understanding of the occurrence of cocaine–opioid interactions at a molecular level. Electrochemical, Raman, and NMR studies of the free drugs and their mixtures were used to study drug–drug interactions. The results were analyzed using data obtained from quantum-mechanical calculations. For the cocaine–morphine mixture (C–MH), formation of a binary complex was detected; this involved the 3-phenolic group and the heterocyclic oxygen of morphine and the carbonyl oxygen and the methyl protons of cocaine’s methyl ester group. NMR studies conducted simultaneously also revealed C–MH binding geometry consistent with theoretical predictions and with electrochemical and vibrational spectroscopy results. These results provide evidence for the occurrence of a cocaine–morphine interaction, both in the solid state and in solution, particularly for the hydrochloride form. A slight interaction, in solution, was also detected by NMR for the cocaine–heroin mixture. Figure "Schematic representation of the proposed model for cocaine:morphine salt interaction