Entropy in molecular recognition by proteins

Abstract

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

“…As such, the backbone typically contains little entropic content. On the other hand, the internal motion of side chains, particularly those bearing methyl groups, has been shown to be heterogeneous and tunable (Caro, et al, 2017; Frederick, et al, 2007; Igumenova, et al, 2006; Kasinath, Sharp, & Wand, 2013; Marlow, et al, 2010), suggesting a rich entropic component. A simplified workflow for determining conformational entropy from NMR-derived measures of fast internal motion is shown in Figure 1.…”

“…Since the spectral density is directly related to NMR-derived spin relaxation parameters, values of O 2 , τ e , and τ m can be extracted by numerical optimization. This is best accomplished using a grid search approach (Dellwo, & Wand, 1989) and various software packages for determining model-free parameters are currently available including software from our laboratory (Caro, et al, 2017). Once optimal model-free parameters have been determined, errors can be estimated using Monte Carlo methods.…”

“…We have recently shown that it is possible to interpret changes in fast dynamics of protein side chains in terms of conformational entropy without debilitating assumptions (Caro, et al, 2017; Wand, & Sharp, 2018). The premise of the entropy meter is that fast (sub-ns) timescale motions report indirectly on the conformational states visited by a protein molecule and that these states reflect either directly or indirectly the overall conformational entropy (Akke, Bruschweiler, & Palmer, 1993; Caro, et al, 2017; Frederick, et al, 2007; Tzeng, & Kalodimos, 2012). Upon a change in functional state, such as the binding of a ligand, the populations of the various states of the ensemble will be redistributed.…”

“…Accordingly, NMR has emerged as a powerful technique for elucidating the temporal changes in structure that mediate a diverse array of protein activities. Of notable interest are the fast picosecond-nanosecond timescale dynamics of protein side chains as these motions have been shown to reflect the considerable residual conformational entropy of folded proteins (Caro, Harpole, Kasinath, Lim, Granja, Valentine et al, 2017). While the role of conformational entropy is still being explored, recent studies suggest it contributes significantly to the free energy of several important protein functions including molecular recognition (Frederick, Marlow, Valentine, & Wand, 2007; Marlow, Dogan, Frederick, Valentine, & Wand, 2010; Takeuchi, Tokunaga, Imai, Takahashi, & Shimada, 2014; Tzeng, & Kalodimos, 2009) and allostery (Capdevila, Braymer, Edmonds, Wu, & Giedroc, 2017; Capdevila, Edmonds, Campanello, Wu, Gonzalez-Gutierrez, & Giedroc, 2018; Popovych, Sun, Ebright, & Kalodimos, 2006).…”

Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

“…3,4 To understand DNA recognition by proteins from a thermodynamic viewpoint, the dynamic properties of basic side chains should be delineated. Some NMR methods have been developed for dynamics investigations of basic side chains.…”