Membrane environment modulates the pKa values of transmembrane helices

The Journal of Physical Chemistry. B
Afra Panahi, Charles L Brooks

Abstract

In this work, we apply the recently developed constant pH molecular dynamics technique to study protonation equilibria of titratable side chains in the context of simple transmembrane (TM) helices and explore the effect of pH on their configurations in membrane bilayers. We observe that, despite a significant shift toward neutral states, considerable population of different side chains stay in the charged state that give rise to pKa values around 9.6 for Asp and Glu and 4.5 to 6 for His and Lys side chains, respectively. These charged states are highly stabilized by favorable interactions between head groups, water molecules, and the charged side chains that are facilitated by substantial changes in the configuration of the peptides. The pH dependent configurations and the measured pKa values are in good agreement with relatively recent solid state NMR measurements. Our results presented here demonstrate that all-atom constant pH molecular dynamics can be applied to membrane proteins and peptides to obtain reliable pKa values and pH dependent behavior for these systems.

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Citations

Feb 11, 2016·Journal of Chemical Theory and Computation·Vitor H TeixeiraMiguel Machuqueiro
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Feb 6, 2020·Proceedings of the National Academy of Sciences of the United States of America·Hedieh TorabifardCharles L Brooks
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Oct 20, 2018·The Journal of Physical Chemistry. B·Piao MaSusan B Rempe

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Methods Mentioned

BETA
NMR

Software Mentioned

CPHMD MSλD

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