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Open Access Research article

Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces

Zhenhua Li1, Ying He1, Limsoon Wong2 and Jinyan Li3*

Author Affiliations

1 Bioinformatics Research Center at the School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore

2 School of Computing, National University of Singapore, Singapore 117417, Singapore

3 Advanced Analytics Institute, University of Technology Sydney, Sydney, Australia

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BMC Bioinformatics 2012, 13:51  doi:10.1186/1471-2105-13-51

Published: 27 March 2012

Abstract

Background

Water is an integral part of protein complexes. It shapes protein binding sites by filling cavities and it bridges local contacts by hydrogen bonds. However, water molecules are usually not included in protein interface models in the past, and few distribution profiles of water molecules in protein binding interfaces are known.

Results

In this work, we use a tripartite protein-water-protein interface model and a nested-ring atom re-organization method to detect hydration trends and patterns from an interface data set which involves immobilized interfacial water molecules. This data set consists of 206 obligate interfaces, 160 non-obligate interfaces, and 522 crystal packing contacts. The two types of biological interfaces are found to be drier than the crystal packing interfaces in our data, agreeable to a hydration pattern reported earlier although the previous definition of immobilized water is pure distance-based. The biological interfaces in our data set are also found to be subject to stronger water exclusion in their formation. To study the overall hydration trend in protein binding interfaces, atoms at the same burial level in each tripartite protein-water-protein interface are organized into a ring. The rings of an interface are then ordered with the core atoms placed at the middle of the structure to form a nested-ring topology. We find that water molecules on the rings of an interface are generally configured in a dry-core-wet-rim pattern with a progressive level-wise solvation towards to the rim of the interface. This solvation trend becomes even sharper when counterexamples are separated.

Conclusions

Immobilized water molecules are regularly organized in protein binding interfaces and they should be carefully considered in the studies of protein hydration mechanisms.