Internal ionizable groups in proteins are essential for many biological processes. They usually have anomalous pvalues. The pvalues of Lys, Asp and Glu at 25 internal positions in staphylococcal nuclease were determined previously in the Garc铆a-Moreno laboratory. Most of th...
PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure. For proteins without ligands, both version should produce the same result. The method is described in the following papers, which you sh...
Such substitutions should affect pKa values without affecting the protein structure. Consistent with our hypothesis, several Gly substitutions were found to shift the pKa values of ionizable groups without affecting the structure noticeably. Efforts are underway to determine what the effects of Gly ...
The PROPKA method for the prediction of the pKa values of ionizable residues in proteins is extended to include the effect of non-proteinaceous ligands on protein pKa values as well as predict the change in pKa values of ionizable groups on the ligand itself. This new version of PROPKA (...
Empirical Method For Calculation of Pka Values of Internal Ionizable Groups in ProteinsAurein 2.2Aurein 2.3Oriented circular dichroismSolid state NMRalpha-Helical structureMembrane interactionMembrane compositionAntimicrobial activityNot Availabledoi:10.1016/j.bpj.2010.12.1454Fitch, Carolyn A....
5. Molecular determinants of pKa values of histidine residues in staphylococcal nuclease. [D] . Baran, Kelli Lynn. 2008 机译:葡萄球菌核酸酶中组氨酸残基pKa值的分子决定因素。 6. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins [O] . Swagata Pahari, ...
The GUI also calculates contributions to the pH-dependent unfolding free energy at a given pH for each ionizable group in the protein. Moreover, the PROPKA-computed pKa values or energy contributions of the ionizable residues in question can be displayed interactively. The PROPKA GUI can also...
In contrast, the pKa of N-terminal α-amino groups of proteins can vary significantly, with reported values between 6.8 and 9.1, raising the possibility that linear chain synthesis may not require a general base. In this study we use NMR spectroscopy to determine the pKa for the N-terminal ...
Background pKa values are a measure of the protonation of ionizable groups in proteins. Ionizable groups are involved in intra-protein, protein-solvent and protein-ligand interactions as well as solubility, protein folding and catalytic activity. The pKa
PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure. For proteins without ligands, both version should produce the same result. The method is described in the following papers, which you sh...