Principles of Biomolecular Recognition

  • Kalju Kahn
  • Kevin W. Plaxco


Biomolecular recognition, the process by which biomolecules recognize and bind to their molecular targets, typically highly specific, high affinity and reversible, and is generalizable to an effectively unlimited range of aqueous analytes. Consequently, it has been exploited in a wide range of diagnostic and synthetic technologies. Biomolecular recognition is typically driven by many weak interactions working in concert. The most important of these interactions include (i) the electrostatic interaction due to permanent charges, dipoles, and quadrupoles, (ii) the polarization of charge distributions by the interaction partner leading to induction and dispersion forces, (iii) Pauli-exclusion principle-derived inter-atomic repulsion, and (iv) a strong, “attractive” force arising largely from the entropy of the solvent and termed the hydrophobic effect. Because the aqueous environment significantly reduces the impact of electrostatic and induction interactions, the hydrophobic effect is often the dominant force stabilizing the formation of correct biomolecule–target complexes. The other effects are nevertheless important in defining the specificity of the macromolecule toward its target by destabilizing binding events in which a less-than-ideal network of interactions between two partners would be established.


Molecular recognition Binding thermodynamics Electrostatic interaction London dispersion Hydrophobic effect 



Coupled cluster singles and doubles


Deoxyribonucleic acid


M½ller–Plesset perturbation theory of the second order


Nuclear magnetic resonance


Ribonucleic acid


Transferable intermolecular potential–4 point



Free energy change


Internal energy change


Entropy change


Enthalpy change


Volume change


Universal gas constant


Absolute temperature




Charge on particle i


Dielectric permittivity of vacuum


Distance between the centers of two objects


Dipole moment


Boltzmann constant


Quadrupole moment




First ionization potential of atom or molecule i


Size parameter in the Lennard-Jones potential


Softness parameter in the Lennard Jones potential; dielectric constant


Planck constant


Vibrational frequency; effective volume of the molecule


Rotational symmetry number


Bjerrum length


Avogadro constant


Refractive index of solute i.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSanta BarbaraUSA

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