KimHummer

The KimHummer potential is a coarse-grained model for protein-protein interactions developed by Kim and Hummer [Hummer2008]. It combines electrostatic interactions with a modified Lennard-Jones potential and includes solvent-accessible surface area (SASA) weighting.

The potential consists of two main terms:

\[U_{KH} = U_{el} + U_{np}\]

where:

  • \(U_{el}\) is the electrostatic term (Debye-Hückel potential)

  • \(U_{np}\) is the non-polar term (modified Lennard-Jones potential)

The electrostatic term is given by the Debye-Hückel potential:

\[U_{el} = \frac{q_i q_j}{4\pi\epsilon_0\epsilon_r} \frac{e^{-r/\lambda_D}}{r}\]

The non-polar term is a modified Lennard-Jones potential:

\[U_{np} = \epsilon_{ij} \left[ \left(\frac{\sigma_{ij}}{r}\right)^{12} - 2\left(\frac{\sigma_{ij}}{r}\right)^6 \right]\]

Both terms are weighted by SASA-dependent factors for each residue.

  • type: NonBonded, KimHummer

  • parameters:

    • cutOffNPFactor: real: Interaction range for non-polar term as a multiple of sigma

    • cutOffDHFactor: real: Interaction range for electrostatics as a multiple of the Debye length

    • dielectricConstant: real: Relative permittivity of the medium \(\epsilon_r\)

    • debyeLength: real: Debye length \(\lambda_D\) \([distance]\)

    • sasaModel: string: SASA weighting model (options: “A”, “B”, “C”, “D”, “E”, “F”)

    • zeroEnergy: real: Energy shift parameter for non-polar term (default: 0.01) \([energy]\)

  • data:

    • name_i: string: Type of residue i

    • name_j: string: Type of residue j

    • epsilon: real: LJ potential well depth \([energy]\)

    • sigma: real: LJ zero-potential distance \([distance]\)

Example:

"kimHummer":{
  "type":["NonBonded","KimHummer"],
  "parameters":{
    "cutOffNPFactor":2.5,
    "cutOffDHFactor":3.0,
    "dielectricConstant":78.5,
    "debyeLength":1.0,
    "sasaModel":"B",
    "zeroEnergy":0.01
  },
  "labels":["name_i", "name_j", "epsilon", "sigma"],
  "data":[
    ["ALA", "ALA", -0.137, 5.0],
    ["ALA", "GLY", -0.068, 4.9],
    ["GLY", "GLY", 0.0, 4.8]
  ]
}

Note

The KimHummer potential requires charge, radius, and SASA information for each particle. Ensure these properties are properly set before using this potential.

[Hummer2008]

Kim, Y. C., & Hummer, G. (2008). Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. Journal of molecular biology, 375(5), 1416-1433.