Workshop on Ion Channels, Tue, 09 Oct, 2007
Speaker: Gernot Kieseritzky
Abstract
pKA in proteins are determined by electrostatic energy computations
using a small number of optimized protein conformations derived from
crystal structures. In these protein conformations hydrogen positions
and geometries of salt bridges on the protein surface were determined
self-consistently with the protonation pattern at three pHs (low,
ambient and high). Considering salt bridges at protein surfaces is most
relevant, since they open at low and high pH. In absence of these
conformational changes, computed of acidic (basic) groups in salt
bridges underestimate (overestimate) experimental pKA dramatically. The
computed pKA for 15 different proteins with 185 known pKA yield an RMSD
of 1.10pK, comparable to (semi)emperical methods. Thus, accounting for
additional conformational flexibility needed to describe the energetics
of salt bridges appropriately. The RMSD of the present approach improves
to 0.97pK, if one considers only the 27 strongly shifted experimental
pKA outperforming the other methods under these conditions.
URL: www.ricam.oeaw.ac.at/specsem/ssqbm/participants/abstracts/index.php
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