Analysis of Protein Binding Sites by Computational Solvent Mapping

  • David R. HallEmail author
  • Dima KozakovEmail author
  • Sandor VajdaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 819)


Computational solvent mapping globally samples the surface of target proteins using molecular probes—small molecules or functional groups—to identify potentially favorable binding positions. The method is based on X-ray and NMR screening studies showing that the binding sites of proteins also bind a large variety of fragment-sized molecules. We have developed the multistage mapping algorithm FTMap (available as a server at based on the fast Fourier transform (FFT) correlation approach. Identifying regions of low free energy rather than individual low energy conformations, FTMap reproduces the available experimental mapping results. Applications to a variety of proteins show that the probes always cluster in important subsites of the binding site, and the amino acid residues that interact with many probes also bind the specific ligands of the protein. The “consensus” sites at which a number of different probes cluster are likely to be “druggable” sites, capable of binding drug-size ligands with high affinity. Due to its sensitivity to conformational changes, the method can also be used for comparing the binding sites in different structures of a protein.

Key words

Protein structure Protein–ligand interactions Binding site Binding hot spots Fragment-based ligand design Druggability Binding site comparison Docking 



This work has been supported by grant GM064700 from the National Institutes of Health.


  1. 1.
    Clackson, T., and Wells, J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267, 383–386.PubMedCrossRefGoogle Scholar
  2. 2.
    Mattos, C., and Ringe, D. (1996). Locating and characterizing binding sites on proteins. Nat. Biotechnol., 14, 595–599.PubMedCrossRefGoogle Scholar
  3. 3.
    Hajduk, P. J., Huth, J. R., and Tse, C. (2005) Predicting protein druggability. Drug Discov Today 10, 1675–1682.PubMedCrossRefGoogle Scholar
  4. 4.
    Hajduk, P.J., Huth, J. R., and Fesik, S. W. (2005). Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 48: 2518–2525.PubMedCrossRefGoogle Scholar
  5. 5.
    Allen, K. N., Bellamacina, C. R., Ding, X., Jeffery, C. J., Mattos, C., Petsko, G. A, Ringe, D. (1996) An experimental approach to mapping the binding surfaces of crystalline proteins J. Phys. Chem. 100: 2605–2611, 1996.Google Scholar
  6. 6.
    English AC, Done SH, Caves LS, Groom CR, Hubbard RE. (1999) Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Proteins 37: 628¯640.PubMedCrossRefGoogle Scholar
  7. 7.
    English AC, Groom CR, Hubbard RE. (2001) Experimental and computational mapping of the binding surface of a crystalline protein. Protein Eng. 14: 47¯59.PubMedCrossRefGoogle Scholar
  8. 8.
    Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. (2006) Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol. 357: 1471–1482.PubMedCrossRefGoogle Scholar
  9. 9.
    Dennis S, Kortvelyesi T, Vajda S. (2002) Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA., 99: 4290–4295, 2002.Google Scholar
  10. 10.
    Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. (2009) Fragment-based identification of druggable “hot spots” of proteins using Fourier domain correlation techniques. Bioinformatics, 25: 621–627.PubMedCrossRefGoogle Scholar
  11. 11.
    Silberstein M, Dennis S, Brown III L, Kortvelyesi T, Clodfelter K, Vajda S. (2003) Identification of substrate binding sites in enzymes by computational solvent mapping, J. Molec. Biol. 332: 1095–1113.PubMedCrossRefGoogle Scholar
  12. 12.
    Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S. (2007) Identification of hot spots within druggable binding sites of proteins by computational solvent mapping. J. Med. Chem., 50: 1231–1240.PubMedCrossRefGoogle Scholar
  13. 13.
    Vajda S, Guarnieri F. (2006) Characterization of protein-ligand interaction sites using experimental and computational methods. Current Opinion in Drug Design and Development 9: 354–362.Google Scholar
  14. 14.
    Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang G-Y, Beglov D, Vajda S, Petsko GA, Ringe D. (2009) Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase, J Comput Aided Mol Des. 23: 491–500.CrossRefGoogle Scholar
  15. 15.
    Landon MR, Amaro RE, Baron R, Ngan C-H, Ozonoff D, McCammon JA, Vajda S. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble, Chem Biol Drug Des 71: 106–116.PubMedCrossRefGoogle Scholar
  16. 16.
    Ngan C-H, Beglov D, Rudnitskay AN, Kozakov D, Waxman DJ, and Vajda, S. (2009) The structural basis of pregnane X receptor binding promiscuity. Biochemistry, 48:11572–11581.PubMedCrossRefGoogle Scholar
  17. 17.
    Chuang, G-Y., Kozakov, D., Brenke, R., Beglov, D., Guarnieri, F., and Vajda, S. (2009) Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel. Biophys. J., 97(10): 2846–2853.PubMedCrossRefGoogle Scholar
  18. 18.
    Congreve M, Aharony D, Albert J, Callaghan O, Campbell J, Carr RA, Chessari G, Cowan S, Edwards PD, Frederickson M, McMenamin R, Murray CW, Patel S, Wallis N. (2007) Application of fragment screening by X-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase. J Med Chem 50:1124–1132.PubMedCrossRefGoogle Scholar
  19. 19.
    Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N. (2007) Application of fragment screening by X-ray crystallography to beta-secretase. J Med Chem 50:1116–1123.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Departments of Biomedical Engineering and Chemistry, Biomolecular Engineering Research CenterBoston UniversityBostonUSA

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