This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and c...

Several pyridoxal-phosphate-dependent enzymes can convert the bound cofactor to pyridoxamine phosphate. This conversion may be an obligatory part of the normal catalytic sequence, as with transaminases, or may be an abnormal path, inactivating the enzyme. This conversion requires protonation of the C(4)' carbon of the cofactor, which has now been shown to proceed stereospecifically and with the...

background l-tryptophan is an important ingredient in medicines, especially in neuromedicines such as antidepressants. many commercial processes employ various microorganisms with high tryptophan synthase activity to produce l-tryptophan from indole and l-serine, but these processes are very costly due to the costs of precursors, especially l-serine. objectives for this reason, we studied the a...

Removal of the heme iron from cytochrome c to generate porphyrin cytochrome c relieves the quenching of porphyrin fluorescence and enhances the fluorescence of the single tryptophan residue and the 4 tyrosine residues. The intensity of the porphyrin fluorescence is not perturbed by denaturation of the protein at neutral pH using either urea or guanidine hydrochloride. However, the amplitude of ...

The solute-solvent interactions of L-glutamic acid and L-methionine have been studied in 0–60% V/V 1,2-propanediolwater media using the pH-metric method. The protonation constants have been calculated with the computer program MINIQUAD75. Selection of the best fit chemical model of the acid-base equilibria is based on standard deviation in protonation constants and residual analysis using cryst...

The data described here supports the research article "Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations" (Soares et al., 2016) [1]. The data involves both standard Molecular Dynamics (MD) and Constant pH Molecular Dynamics (CpHMD) to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation. The data obtained from MD simulation d...

We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation st...

The protonation constants of L-Aspartic acid have been studied pH-metrically in various concentrations (0-60% v/v) of acetonitrile- and ethylene glycol-water mixtures maintaining an ionic strength of 0.16 mol L-1 at 303K. The protonation constants have been calculated with the computer program MINIQUAD75 and are selected based on statistical parameters. Linear variation of step-wise protonation...

An explicit application of isodesmic reaction (a proton exchange between the studied and similar in structure reference molecule), where the free energy change of the protonation reaction in water was obtained using the free energies in solution from a single continuum model, was used to predict stepwise protonation constants of nitrilotriacetic acid. Calculations were performed at the RB3LYP/6...