A1 Journal article (refereed)
What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations (2024)

Aho, N., Groenhof, G., & Buslaev, P. (2024). What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations. Journal of Physical Chemistry B, Early online. https://doi.org/10.1021/acs.jpcb.4c05947

JYU authors or editors

Publication details

All authors or editors: Aho, Noora; Groenhof, Gerrit; Buslaev, Pavel

Journal or series: Journal of Physical Chemistry B

ISSN: 1520-6106

eISSN: 1520-5207

Publication year: 2024

Publication date: 31/10/2024

Volume: Early online

Publisher: American Chemical Society

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1021/acs.jpcb.4c05947

Publication open access: Not open

Publication channel open access: 

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/98470

Abstract

X-ray crystallography is an important technique to determine the positions of atoms in a protein crystal. However, because the native environment in which proteins function, is not a crystal, but a solution, it is not a priori clear if the crystal structure represents the functional form of the protein. Because the protein structure and function often depend critically on the pH, the question arises whether proton affinities are affected by crystallization. X-ray diffraction usually does not reveal protons, which makes it difficult to experimentally measure pKa shifts in crystals. Here, we investigate whether this challenge can be addressed by performing in silico titration with constant pH molecular dynamics (MD) simulations. We compare the computed pKa values of proteins between solution and crystal environment and analyze these differences in the context of molecular interactions. For the proteins considered in this work, pKa shifts were mostly found for residues at the crystal interfaces, where the environment is more apolar in the crystal than in water. Although convergence was an obstacle, our simulations suggest that in principle it is possible to apply constant pH MD to protein crystals routinely and assess the effect of crystallization on protein function more systematically than with standard MD simulations. We also highlight technical challenges that need to be addressed to make MD simulations of crystals more reliable.

Keywords: crystals; reaction mechanisms; peptides; proteins; x-ray crystallography

Free keywords: crystal structure; crystals; monomers; peptides and proteins; reaction mechanisms

Contributing organizations

Ministry reporting: Yes

VIRTA submission year: 2024

Preliminary JUFO rating: 1