Water in protein structure prediction

Garegin A. Papoian, Johan Ulander, Michael P. Eastwood, Zaida Luthey-Schulten, Peter G. Wolynes

Research output: Contribution to journalArticlepeer-review


Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins. Free energy profile analysis suggests that long-range water-mediated potentials guide folding and smooth the underlying folding funnel. Analyzing simulation trajectories gives direct evidence that water-mediated interactions facilitate native-like packing of supersecondary structural elements. Long-range pairing of hydrophilic groups is an integral part of protein architecture. Specific water-mediated interactions are a universal feature of biomolecular recognition landscapes in both folding and binding.

Original languageEnglish (US)
Pages (from-to)3352-3357
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number10
StatePublished - Mar 9 2004

ASJC Scopus subject areas

  • General


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