The Origins of Femtomolar Protein−Ligand Binding:  Hydrogen-Bond Cooperativity and Desolvation Energetics in the Biotin−(Strept)Avidin Binding Site

Abstract

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each -NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

“…In the passing, it should be mentioned that the predicted number of water molecules in the bound and unbound state matches what have been found in the related streptavidin protein, both by experiment and calculations. 73,74,75 For the ligand-free state, the SASA estimate of  G np free is 11 kJ/mol too negative, whereas the PCM and CD estimates are 1-3 kJ/mol too positive. The total  G np is well reproduced by both CD(P0) and PCM(P0) with errors of 2-3 kJ/mol, whereas SASA(P0) has an error of 13 kJ/mol.…”

Strong Short‐Range Cooperativity in Hydrogen‐Bond Chains

“…Furthermore, the limited range of the cooperative effect was consistent with previous computations suggesting that polarization changes most rapidly at the ends of H‐bond chains 4c, 9b, 16, 17. Our findings have implications for the fundamental understanding, modeling, and exploitation of H‐bond chains particularly in regard to their role in catalysis,4d and in determining molecular structures and recognition properties 5a, 17c, 20. One might speculate that biology has already explored energetic cooperativity in phenolic H‐bond chains, considering that catechol, not pyrogallol, moieties (Figure 1 B) have been selected by evolution for their adhesive properties 11e, 11f…”

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

“…The ligands are shown in Figure 1. The avidinbiotin and lysozyme-benzene systems have been the subject of several previous theoretical studies [21,33,34,35,36,37,38,39,40,41,42,43,44,45],…”

“…Avidin has one histidine residue in each subunit of the tetrameric protein, and it was normally (i.e. when it was not allowed to titrate) assumed to be protonated on the ND1 atom [39]. FXa has six histidine residues, three of which were normally assumed to be protonated on NE2, two on ND1, and one double protonated [40].…”