Modeling methods for studying post-translational and transcriptional modifying enzymes

Studying the phosphoryl transfer mechanism of theE. coliphosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations

“…Once the converged MFEPs were determined, the corresponding potentials of mean force (PMFs) were obtained using the umbrella sampling method47 along the path CVs39,45 that define the progress of the system along these paths. This methodological combination has proven to be an efficient approach for studying the free energy landscapes of complex enzymatic reactions 39,48,49. Details related with the simulations performed are widely described on the ESI †…”

E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft

“…Addition of a phosphate group to serine, threonine or tyrosine residues can induce large conformational modifications in proteins 8 9 10 11 12 13 14 15 16 17 18 . This is driven by electrostatic perturbation or steric hindrance, which can affect the protein energy landscape, intermolecular protein-ligand interactions and enzymatic activity 18 19 20 21 22 . In addition to the critical role of phosphorylation in normal cellular function, aberrant regulation of phosphorylation-induced electrostatic switches is involved in numerous pathologies, such as cancers 23 24 25 .…”

Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase

“…After obtaining the MFEP, a path collective variable , was defined to obtain the potential of mean force (PMF) using umbrella sampling . This methodological combination offers an efficient approach for studying the free energy landscape of complex enzymatic reactions . The active space selected to trace the MFEP was formed by the distances S–CH 3 , CH 3 –N6, N6–H62, and H62–OδAsn105 for the reaction mechanism where the Asn105 abstracts the proton and S–CH 3 , CH 3 –N6, N6–H61, and H61–O w for the process where the water molecule is the proton acceptor.…”

“…48 This methodological combination offers an efficient approach for studying the free energy landscape of complex enzymatic reactions. 49 The active space selected to trace the MFEP was formed by the distances S−CH 3 , CH 3 −N6, N6− H62, and H62−OδAsn105 for the reaction mechanism where the Asn105 abstracts the proton and S−CH 3 , CH 3 −N6, N6− H61, and H61−O w for the process where the water molecule is the proton acceptor. A total of 30 string nodes was used to trace the MFEP for each reaction mechanism, and the values employed for the force constant and friction in the string method were K = 6000 kJ•mol −1 •Å −2 , γ = 9000 ps −1 , respectively.…”