Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC. / Bizkaia:Talent and the European Union's Seventh Framework Program (Marie Curie Actions; COFUND; to S.C., A.S., T.K.); Marie Curie Actions Career Integration Grant (PCIG14-GA-2013-632072 to P.F.); Ministerio de Economía Y Competitividad (CTQ2014-55907-R to P.F., S.C.); FIRB Futuro in Ricerca from the Italian Ministero dell'Istruzione, dell'Universitá e della Ricerca (RBFR130VS5_001 to A.F.); Peruvian Programa Nacional de Innovación para la Competitividad y Productividad (382-PNICP-PIBA-2014 (to P.M. and A.F.)). Funding for open access charge: Institutional funding. / Revisión por pares

Made available in DSpace on 2014-12-17T14:10:24Z (GMT). No. of bitstreams: 1 JonasINO_DISSERT.pdf: 890224 bytes, checksum: a68b1b3f5f169bb87b98314d116a12b3 (MD5) Previous issue date: 2012-03-02 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicos?dico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced. / Nessa disserta??o, os princ?pios te?ricos que regem a Modelagem Molecular foram aplicados na caracteriza??o eletr?nica do oligopept?deo α3 e seus variantes (5Q,7Q)-α3, como tamb?m na descri??o qu?ntica da intera??o do aminoglicos?deo higromicina B e a subunidade 30S do ribossomo bacteriano. No primeiro estudo, os dipept?deos lineares e neutros constituintes das biomol?culas mencionados foram modelados e posteriormente otimizados at? uma estrutura de menor energia potencial e ?ngulos diedros adequados. No caso, tr?s processos de otimiza??o geom?trica, baseados subsequentemente na teoria cl?ssica newtoniana, na semi-emp?rica e na teoria do funcional da densidade (DFT), varreram a paisagem de energia de cada dipept?deos na busca de uma estrutura de energia m?nima ideal. Por fim, os conf?rmeros ?timos foram descritos quanto ao potencial eletrost?tico, energia de ioniza??o (amino?cidos), orbitais de fronteira HOMO/HOMO-1 e termo de hopping. A partir dos termos de hopping descritos nesse trabalho, foi poss?vel, em estudos subsequentes, caracterizar as propriedades de transporte de cargas destes modelos pept?dicos. Vislumbra-se uma nova tecnologia de biosensores capaz de diagnosticar doen?as amiloides, relacionadas ao ac?mulo de pept?deos disformes, a partir do perfil de condutividade el?trica apresentado pelas prote?nas do paciente. Em um segundo momento dessa disserta??o, realiza-se um estudo qu?ntico por modelagem molecular da energia de intera??o de um antibi?tico aminoglicos?dico em seu receptor riboss?mico. Sabe-se que a higromicina B (higB) ? um antibi?tico aminoglicos?deo que afeta a transloca??o ribossomal pela intera??o direta com a subunidade menor do ribossomo bacteriano (30S), especificamente com nucleot?deos da h?lice 44 do RNA riboss?mico 16S (rRNA 16S). Devido ao forte car?ter eletrost?tico desta conex?o, foi proposta a investiga??o energ?tica do mecanismo de liga??o da higB no 30S usando diferentes valores de constantes diel?tricas (ε=0, 4, 10, 20 e 40), as quais s?o amplamente utilizadas no estudo das propriedades eletrost?ticas de biomol?culas. Para isso, foram medidos raios crescentes centralizados no centr?ide da higB tendo por base a estrutura cristalina higB-30S (1HNZ.pdb), e apenas a energia de intera??o individual de cada nucleot?deo englobado foi calculada quanticamente utilizando a estrat?gia de fracionamento molecular com capuzes conjugados (MFCC). Percebeu-se que as constantes diel?tricas subestimam as energias de intera??o individuais, permitindo que o estado de converg?ncia energ?tica seja alcan?ado rapidamente. Por?m apenas para ε=40, a energia de intera??o total droga-receptor se estabilizou em r=18?, o que se constituiu como um adequado s?tio de liga??o, pois englobou os res?duos do 16S que interagem mais fortemente com a higB - C1403, C1404, G1405, A1493, G1494, U1495, C1496 e U1498. Assim, a constante diel?trica ≈40 ? ideal para o tratamento de sistemas com muitas cargas. Confrontando as energias de liga??o individuais dos nucleot?deos 16SrRNA com ensaios experimentais para determina??o da concentra??o inibit?ria m?nima (MIC) da higB, acredita-se que esses res?duos com elevados valores de intera??o gerariam resist?ncia bacteriana ? droga quando mutados. Com o mesmo racioc?nio, visto que aqueles com baixa energia n?o influenciariam de forma eficaz a afinidade da higB em seu s?tio de liga??o, n?o ocorreria perda de efic?cia caso fossem substitu?dos.