Skip to main content
Article thumbnail
Location of Repository

‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces

By Jinyan Li and Qian Liu

Abstract

Motivation: The O-ring theory reveals that the binding hot spot at a protein interface is surrounded by a ring of residues that are energetically less important than the residues in the hot spot. As this ring of residues is served to occlude water molecules from the hot spot, the O-ring theory is also called ‘water exclusion’ hypothesis. We propose a ‘double water exclusion’ hypothesis to refine the O-ring theory by assuming the hot spot itself is water-free. To computationally model a water-free hot spot, we use a biclique pattern that is defined as two maximal groups of residues from two chains in a protein complex holding the property that every residue contacts with all residues in the other group

Topics: Original Papers
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2654803
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Citations

    1. (1995). A hot spot of binding energy in a hormone-receptor interface.
    2. (2006). A lock-and-key model for protein-protein interactions.
    3. (2004). A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications.
    4. (2005). A protein domain interaction interface database: interpare.
    5. (2003). Analysing six types of protein-protein interfaces.
    6. (1998). Anatomy of hot spots in protein interfaces.
    7. (2004). Anchor residues in protein–protein interactions.
    8. (1994). Arboricity and bipartite subgraph listing algorithms.
    9. (2001). Asedb: a database of alanine mutations and their effects on the free energy of binding in protein interactions.
    10. (1998). Bipartite Graphs and their Applications.
    11. (2006). Characterization and prediction of protein–protein interactions within and between complexes.
    12. (2003). Dehydron: a structurally encoded signal for protein interaction.
    13. (1998). Dictionary of interfaces in proteins (dip): data bank of complementary molecular surface patches.
    14. (2006). Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale.
    15. (2005). Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions.
    16. (2005). Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues.
    17. (2008). Hotsprint: database of computational hot spots in protein interfaces.
    18. (2008). Interacting amino acid preferences of 3d pattern pairs at the binding sites of transient and obligate protein complexes.
    19. (2005). Localization of protein-binding sites within families of proteins.
    20. (2007). Maximal biclique subgraphs and closed pattern pairs of the adjacency matrix: a one-to-one correspondence and mining algorithms.
    21. (1998). Morphology of protein–protein interfaces.
    22. (2006). Noxclass: prediction of protein–protein interaction types.
    23. (2005). Pibase: a comprehensive database of structurally defined protein interfaces.
    24. (1975). Principles of protein-protein recognition.
    25. (1996). Principles of protein–protein interactions.
    26. (2004). Protein-protein interactions: coupling of structurally conserved residues and of hot spots across interfaces—implications for docking.
    27. (2004). Protein–protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states–implications for docking.
    28. (1993). Shape complementarity at protein/protein interfaces.
    29. (2004). Structure-based method for analyzing protein–protein interfaces.
    30. (2005). Structure, function, and evolution of transient and obligate protein–protein interactions.
    31. (1997). Studies of protein–protein interfaces: a statistical analysis of the hydrophobic effect.
    32. (2002). The Pymol User’s Manual. Delano Scientific,
    33. (2002). Unraveling hot spots in binding interfaces: progress and challenges.
    34. (2007). What drives proteins into the major or minor grooves of dna?

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.