Learning about Biomolecular Solvation from Water in Protein Crystals.

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2018-03

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Altan, Irem
Fusco, Diana
Afonine, Pavel V
Charbonneau, Patrick

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Abstract

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

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10.1021/acs.jpcb.7b09898

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Altan, Irem, Diana Fusco, Pavel V Afonine and Patrick Charbonneau (2018). Learning about Biomolecular Solvation from Water in Protein Crystals. The journal of physical chemistry. B, 122(9). pp. 2475–2486. 10.1021/acs.jpcb.7b09898 Retrieved from https://hdl.handle.net/10161/24993.

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Scholars@Duke

Charbonneau

Patrick Charbonneau

Professor of Chemistry

Professor Charbonneau studies soft matter. His work combines theory and simulation to understand the glass problem, protein crystallization, microphase formation, and colloidal assembly in external fields.


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