Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comment
. 2004 Mar 9;101(10):3325-6.
doi: 10.1073/pnas.0400157101. Epub 2004 Mar 1.

Water and proteins: a love-hate relationship

Yaakov Levy  1 , José N Onuchic
Affiliations
Comment

Water and proteins: a love-hate relationship

Yaakov Levy et al. Proc Natl Acad Sci U S A. .
No abstract available

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
The knowledge-based potentials incorporated in the structure prediction Hamiltonian by Papoian et al. (1). Each pair of residues can interact directly or meditatively by a water molecule (these two types of contacts are also termed first and second wells, respectively). A direct contact was defined as occurring between residues when the distance between their Cβ atoms is 4.5–6.5 Å, and, similarly, a water-mediated contact was set to a distance of 6.5–9.5 Å. The second well includes also a protein-mediated contact potential (data not shown), which is highly correlated with the direct-contact potential. Positive values indicate more favorable interactions.
Fig. 2.
Fig. 2.
Water at the protein–protein and protein–DNA interfaces. The complex of bovine papilloma-virus-1 E2 with DNA (PDB ID code 2bop) contains 241 water molecules (represented by spheres), of which 40 water molecules mediate protein–protein interactions (blue spheres) and another 42 water molecules mediate protein–DNA interactions (light blue spheres).
See this image and copyright information in PMC

Comment on

  • Water in protein structure prediction.
    Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Papoian GA, et al. Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3352-7. doi: 10.1073/pnas.0307851100. Epub 2004 Feb 26. Proc Natl Acad Sci U S A. 2004. PMID: 14988499 Free PMC article.

References

    1. Papoian, G. A., Ulander, J., Eastwood, M. P., Luthey-Schulten, Z. & Wolynes, P. G. (2004) Proc. Natl. Acad. Sci. USA 101, 3352-3357. - PMC - PubMed
    1. Savage, H. & Wlodawer, E. (1986) Methods Enzymol. 127, 162-183. - PubMed
    1. Ernst, J. A., Clubb, R. T., Zhou, H.-X., Gronenborn, A. M. & Clore, G. M. (1995) Science 267, 1813-1817. - PubMed
    1. Otting, G., Liepinsh, E. & Wuthrich, K. (1991) Science 254, 974-980. - PubMed
    1. Pal, S. K., Peon, J. & Zewail, A. H. (2002) Proc. Natl. Acad. Sci. USA 99, 1763-1768. - PMC - PubMed

Publication types

LinkOut - more resources