Molecular modeling of enzyme attachment on AFM probes

Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors

“…The use of a rigid model is justified based on the stability of the dimeric structures. Indeed, a stable dimeric ACC structure was reached within 10 ns of MD trajectory with a RMSD of 0.3 nm [19], whereas the dimeric structure was attached to a functionalized surface, it remained stable within a RMSD of 0.35 nm after a 50 ns MD trajectory [20].…”

“…1, was obtained from the Protein Data Bank online repository [18] under PDB ID 1UYR. The enzyme was assumed to adopt a dimeric conformation in solution, according to molecular dynamics simulation with an all-atom model [19,20]. The coverage of the AFM tip with the enzymes was simulated with a stochastic process in MD simulations, where a coarse-grained model had to be used.…”

Development of an Enzyme-Coated Microcantilever-Based Biosensor for Specific Detection of Short-Chain Alcohols

“…The functionalization through the formation of the self-assembled monolayer (SAM) activated with APTES [16,18,19] was performed with alcohol dehydrogenase enzyme stock solution (0.25 mg/mL) dissolved in 50 mM sodium phosphate buffer, pH 8.6.…”

Aplicações de química teórica no estudo de materiais: métodos in silico para nanomateriais

“…Nesse contexto, as técnicas computacionais que podem ser utilizadas para complementar os resultados experimentais são: (i) Modelagem por Homologia; (ii) Docking Molecular; (iii) DM; (iv) Mecânica Quântica e os cálculos híbridos de QM/ MM (Mecânica Quântica e Mecânica Molecular); e (v) Dinâmica Molecular Direcionada (SMD, do inglês Steered Molecular Dynamics). 21 Amarante et al (2014), Oliveira et al (2013). 22 Amarante et al (2014).…”