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Review
. 2009 Sep;109(9):4092-107.
doi: 10.1021/cr800551w.

Theory of free energy and entropy in noncovalent binding

Huan-Xiang Zhou  1 , Michael K Gilson
Affiliations
Review

Theory of free energy and entropy in noncovalent binding

Huan-Xiang Zhou et al. Chem Rev. 2009 Sep.
No abstract available

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Figures

Figure 1
Figure 1
An interpretation of the standard binding free energy. Upon binding, the volume available to the ligand is changed from V∘ to Vb. At the same time, the ligand gains interaction energy W0.
Figure 2
Figure 2
(A) Diagram of a receptor-ligand potential of mean force W(r, ω), shown as an energy surface in two dimensions with the bound state defined by the deep energy well. The boundary of the bound state can be specified by an upper bound, indicated by a green ring, of W(r, ω) so long as the well is only big enough to hold a single ligand at a time. (B) Sketch of the binding constant associated with the energy well in (A) as a function of the upper bound of W(r, ω). The binding constant is seen to be virtually independent of the upper bound so long as the lowest energy configurations are included.
Figure 3
Figure 3
The entropy of binding and its parts for a diatomic binding model according to the RRHO approximation. The entropy of binding in the FM approach is also shown for comparison. As also labeled in the figure, from top to bottom on the left axis the graphs are: ΔSRRHO, r; ΔSRRHO, vib in the quantum and classical formulations, respectively; ΔSRRHO∘ in the quantum formulation; ΔSt∘;ΔSRRHO∘ in the classical formulation; and ΔSRRHO,t∘. The results are derived in Subsection 2.2 of Supporting Information.
Figure 4
Figure 4
(A) A receptor (orange) and ligand (green) connected by a linker (black), showing the position vector, r, relating the ligand to the receptor, and the orientation of the ligand in space ω. In the bound state r takes the value r0. (B) Binding of a bivalent ligand can be viewed as the sequential binding of the first fragment followed by intramolecular binding of the second.
See this image and copyright information in PMC

References

    1. Gilson MK, Zhou HX. Annu Rev Biophys Biomol Struct. 2007;36:21. - PubMed
    1. Hay BP, Firman TK. Inorg Chem. 2002;41:5502. - PubMed
    1. Bryantsev VS, Hay BP. J Am Chem Soc. 2006;128:2035. - PubMed
    1. Chen W, Gilson MK. J Chem Inf Model. 2006;47:425. - PubMed
    1. Kamper A, Apostolakis J, Rarey M, Marian CM, Lengauer T. J Chem Inf Model. 2006;46:903. - PubMed

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