Principles of Biomolecular Recognition

Chapter

Abstract

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.

Keywords

Molecular recognition Binding thermodynamics Electrostatic interaction London dispersion Hydrophobic effect 

Abbreviations

CCSD

Coupled cluster singles and doubles

DNA

Deoxyribonucleic acid

MP2

M½ller–Plesset perturbation theory of the second order

NMR

Nuclear magnetic resonance

RNA

Ribonucleic acid

TIP4P

Transferable intermolecular potential–4 point

Symbols

ΔG

Free energy change

ΔU

Internal energy change

ΔS

Entropy change

ΔH

Enthalpy change

ΔV

Volume change

R

Universal gas constant

T

Absolute temperature

F

Force

qi

Charge on particle i

ε0

Dielectric permittivity of vacuum

r

Distance between the centers of two objects

μ

Dipole moment

k

Boltzmann constant

Θ

Quadrupole moment

α

Polarizability

Ii

First ionization potential of atom or molecule i

σ

Size parameter in the Lennard-Jones potential

ε

Softness parameter in the Lennard Jones potential; dielectric constant

h

Planck constant

v

Vibrational frequency; effective volume of the molecule

σ

Rotational symmetry number

λB

Bjerrum length

NA

Avogadro constant

ni

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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