The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

Mechanisms underlying congenital malformations are largely unknown despite its high incidence, affecting 2-3% of liveborn infants. A broader knowledge about the causes of birth defects would provide valuable information regarding the outcome and prognosis of the anomaly, the development and establishment of diagnostic protocols, the design of therapeutic strategies and genetic counseling to the family. Different approaches have been used in the present thesis regarding technologies and model diseases to elucidate the contribution of genetic and epigenetic alterations in the etiopathogenesis of congenital malformations. Copy number variations, methylation patterns, as well as point mutations have been explored. Moreover, a study to analyze genetic counseling in relation to one of the new molecular techniques used has been performed. Obtained data reveal a relevant role of genetic and epigenetic alterations in congenital malformations, in some cases as a unique cause to explain the disease and in others as part of an oligogenic or multifactorial model. / Els mecanismes causants de les malformacions congènites són poc coneguts malgrat l’elevada incidència d’aquestes patologies, que afecten el 2-3% de recent nascuts. Un coneixement més ampli de les causes de les anomalies congènites proporcionaria informació rellevant pel que fa al pronòstic de l’anomalia, el desenvolupament i establiment de protocols diagnòstics, el disseny d’estratègies terapèutiques, així com l’assessorament genètic a la família. En la tesi que es presenta s’han utilitzat diferents estratègies, pel que fa a tecnologies i models de malalties, amb l’objectiu d’esbrinar la contribució d’alteracions genètiques i epigenètiques en l’etiopatogènia de les malformacions congènites. S’han analitzat variacions en número de còpia, patrons de metilació, així com mutacions puntuals. D’altra banda, també s’ha realitzat un estudi per aprofundir en l’assessorament genètic en relació a una de les noves tècniques moleculars utilitzades. Els resultats obtinguts indiquen que les altercacions genètiques i epigenètiques tenen una contribució molt rellevant en l’etiologia de les malformacions congènites, en alguns casos com a causa única de la malaltia i en altres com a component d’un model oligogènic o multifactorial.