Intermolecular forces between macromolecules govern many biological processes. One such process is protein-ligand binding andunbinding.The avidin-biotin complex, known for its extremelyhigh affinity [63], has been experimentally studied more extensively than most other protein-ligand systems.Apart from itsbiological importance, the avidin-biotin complex is an excellenttool in various experiments such as affinity chromatography, affinity cytochemistry, biosensors, diagnostics, targeted drug delivery[64, 65, 66], and immunoassays [67]. Avidin isolated from hen egg-white [68] is a tetrameric glycoprotein comprising almost 8000atoms, which can bind up to fourmolecules of biotin.Biotin is a 32-atom vitamin which acts asa carrier of activated CO2 in some biochemical reactions.The2.7 A resolution crystal structure of the avidin-biotin complexhas been reported recently [69, 70, 71].With the avidin-biotinadhesion force directly measured with atomic force microscope(AFM) techniques [72, 73, 74], the data produced by computersimulations can be compared to experimental observations. We performed molecular dynamics simulations of the avidin-biotin complex using the program X-PLOR[23] with the CHARMM22force field and implemented the external force acting on the system through addition of an artificial harmonic potential kx2 withk increasing linearly in time from zero to some maximum value. Our simulations demonstrate that the hydrogen bonds yield themajor contribution to the binding, the strongest bond of about10 kcal/mole being formed by Tyr33. However, hydrophobic interactions between biotin and non-polar residues in the bindingpocket, three tryptophans and a phenylalanine, contribute about1/4 of the total avidin-biotin interaction energy. Currently we are carrying out MD simulations of the avidin-biotincomplex rupture for time scales of several hundred picoseconds,which may allow us to extrapolate the forces to the experimental value (millisecond timescale). Related simulations have beenrecently carried out on streptavidin [75]. We also plan to investigate avidin mutants and compare our results to the data obtained experimentally for streptavidin mutants.
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