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Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.

Dynamical effects have recently received much attention in the context of the theoretical investigation of enzymatic catalysis. In this paper we use a combination of Grote−Hynes theory with quantum mechanical/molecular mechanical modeling that is a powerful tool to understand and quantify these dynamical effects in a particular enzyme, the glycine N-methyltransferase (GNMT). Comparison of the results obtained for this enzyme with another methyltransferase (catechol O-methyltransferase, COMT) allows us to understand the different nature of the coupling of the environment to the reaction coordinate as a function of the electrostatic interaction established by the reactive subsystem. The transmission coefficients obtained using Grote−Hynes theory are in excellent agreement with molecular dynamics estimations and show that the coupling is higher in GNMT than in COMT. The larger friction observed in GNMT is explained on the basis of the interaction established by the substrate in the active site. The larger value of the friction leads to a smaller value of the reaction frequency and thus also to a larger disagreement with the estimation of the transmission coefficient based on the frozen environment approach.

The interaction between histamine and highly polymerized calf-thymus DNA has been investigated using FT-Raman spectroscopy and the hybrid QM/MM (quantum mechanics/molecular mechanics) methodology. Raman spectra of solutions containing histamine and calf-thymus DNA, at different molar ratios, were recorded. Solutions were prepared at physiological settings of pH and ionic strength, using both natural and heavy water as the solvent. The analysis of the spectral changes on the DNA Raman spectra when adding different concentrations of histamine allowed us to identify the reactive sites of DNA and histamine, which were used to built two minor groove and one intercalated binding models. They were further used as starting points of the QM/MM theoretical study. However, minimal energy points were only reached for the two minor groove models. For each optimized structure, we calculated analytical force constants of histamine molecule in order to perform the vibrational dynamics. Normal mode descriptions allowed us to compare calculated wavenumbers for DNA-interacting histamine to those measured in the Raman spectra of DNA–histamine solutions. � 2005 Elsevier B.V. All rights reserved.

Combined quantum mechanics/molecular mechanics molecular dynamics simulations have been carried out to study the cleavage of the carbon–chlorine bond in 1,2-dichloroethane catalysed by haloalkane dehalogenase from Xanthobacter Autotrophicus GJ10. The process has been compared with an adequate counterpart in aqueous solution, the nucleophilic attack of acetate anion on 1,2-dichloroethane. Within the limitations of the model, mainly due to the use of a semiempirical Hamiltonian, our results reproduce the magnitude and characteristics of the catalytic effect. Comparisons of the enzymatic and in solution potentials of mean force reveal that, irrespective of the reference state, the enzyme shows a larger affinity for the transition state. The origin of this increased affinity is found in the differences in the electrostatic pattern created by the environment in aqueous solution and in the enzyme.

The dissociative electron transfer reaction CH3Cl+e−→CH3•+Cl− in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem (a methylchloride molecule plus an electron) is described using density functional theory while the solvent (300 water molecules) is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force (PMF) for the carbon–chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Marcus’ relationship, originally developed for electron transfer processes not involving bond breaking. We also investigated dynamical aspects by means of 60 dissociative trajectories started with the addition of an extra electron to different configurations of a methylchloride molecule in solution. The PMF shows the existence of a very flat region, in which the system is trapped during some finite time if the quantum subsystem quickly losses its excess kinetic energy transferring it to the solvent molecules. One of the most important factors determining the effectiveness of this energy transfer seems to be the existence of close contacts (hydrogen bonds) between the solute and the solvent. Estanislao.Silla@uv.es Ignacio.Tunon@uv.es

1,2-Dichoroethane (DCE) is a prototypical molecule for studying electrostatic solvent effects on molecular conformation as far as rotation around the carbon−carbon bond notably changes the electric...