Browsing by Subject "pKa"

Now showing items 1-3 of 3

Article

Direct detection of Fe(IV)=O intermediates in the cytochrome aa3 oxidase from Paracoccus denitrificans[H2O2 reaction

Pinakoulaki, Eftychia; Pfitzner, U.; Ludwig, B.; Varotsis, Constantinos (2003)

We report the first evidence for the formation of the "607- and 580-nm forms" in the cytochrome oxidase aa3/H2O2 reaction without the involvement of tyrosine 280. The pKa of the 607-580-nm transition is 7.5. The 607-nm ...
Article

Proteus and the design of ligand binding sites

Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)

This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...
Article

Proton binding to proteins: A free-energy component analysis using a dielectric continuum model

Archontis, Georgios Z.; Simonson, T. (2005)

Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...