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Protein-protein interactions: Coupling of structurally conserved residues and of hot spots across interfaces. implications for docking

  1. Author:
    Halperin, I.
    Wolfson, H.
    Nussinov, R.

  2. Author Address

    Nussinov, R, Tel Aviv Univ, Sackler Sch Med, Sackler Inst Mol Med, Dept Human Genet & Mol Med, IL-69978 Tel Aviv, Israel Tel Aviv Univ, Sackler Sch Med, Sackler Inst Mol Med, Dept Human Genet & Mol Med, IL-69978 Tel Aviv, Israel. Tel Aviv Univ, Sch Comp Sci, Fac Exact Sci, IL-69978 Tel Aviv, Israel. SAIC Frederick Inc, Basic Res Program, Lab Expt & Computat Biol, Frederick, MD 21702 USA.
    1. Year: 2004
  2. Journal: Structure
    1. 12
    2. 6
    3. Pages: 1027-1038
  4. Type of Article: Article
  1. Abstract:

    Hot spot residues contribute dominantly to protein-protein interactions. Statistically, conserved residues correlate with hot spots, and their occurrence can distinguish between binding sites and the remainder of the protein surface. The hot spot and conservation analyses have been carried out on one side of the interface. Here, we show that both experimental hot spots and conserved residues tend to couple across two-chain interfaces. Intriguingly, the local packing density around both hot spots and conserved residues is higher than expected. We further observe a correlation between local packing density and experimental DeltaDeltaG. Favorable conserved pairs include Gly coupled with aromatics, charged and polar residues, as well as aromatic residue coupling. Remarkably, charged residue couples are underrepresented. Overall, protein-protein interactions appear to consist of regions of high and low packing density, with the hot spots organized in the former. The high local packing density in binding interfaces is reminiscent of protein cores

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