Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper

Abstract

In solution proteins often exhibit backbone and side‐chain flexibility. Yet electrostatic interactions in proteins are sensitive to motions. Hence, here we study the contribution of ion pairs toward protein stability in a range of conformers which sample the conformational space in solution. Specifically, we focus on the electrostatic contributions of ion pairs to the stability of each of the conformers in the NMR ensemble of the c‐Myc‐Max leucine zipper and to their average energy minimized structure. We compute the electrostatic contributions of inter‐ and intra‐helical ion pairs and of an ion pair network. We find that the electrostatic contributions vary considerably among the 40 NMR conformers. Each ion pair, and the network, fluctuates between being stabilizing and being destabilizing. This fluctation reflects the variability in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other and with respect to other charged groups in the rest of the protein. Ion pair interactions in the c‐Myc‐Max leucine zipper in solution depend on the protein conformer which is analyzed. Hence, the overall stabilizing (or destabilizing) contribution of an ion pair is conformer population–dependent. This study indicates that free energy calculations performed using the continuum electrostatics methodology are sensitive to protein conformational details. Proteins 2000;41:485–497. © 2000 Wiley‐Liss, Inc.

How do thermophilic proteins deal with heat?

“…Salt bridges with favorable geometrical positioning of the interacting side chain charged groups are likely to stabilize the protein structure. These observations have gained further support from our recent work in this direction [90,91,Kumar and Nussinov, unpublished data].…”

“…Protein flexibility is essential for function. Our recent investigations into the role of electrostatic interactions in systemic protein flexibility [90,91] have shown that salt bridges and their networks observed in protein crystal structures may easily break and reform in CMLS, Cell. Mol.…”

Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase

“…Interhelical ion pairs have been described as either having no effect on stability or being slightly destabilizing25, 49, 50 or being stabilizing 51, 52. The electrostatic free energy of salt bridges was shown to change sign at least once across 40 NMR conformers of the c‐Myc‐Max leucine zipper 53. From the analysis of a large set of ion pairs, it was concluded that stabilizing or destabilizing effects are governed not only by the mutual geometrical orientation of the participating charged groups but are also very sensitively dependent on the exact distribution of full and partial charges in the protein matrix 54.…”

Close-Range Electrostatic Interactions in Proteins

“…The availability of multiple protein structures for the same protein is valuable in studying protein flexibility. In our studies,2b,2c we have used NMR conformer ensembles and protein crystal structures to study systemic protein flexibility. Figure 1 provides an example of protein flexibility and illustrates individual conformers in the NMR conformer ensemble of the Escherichia coli chemotaxis protein CheY as well as its crystal structures.…”

“…All the ion pairs and the ion‐pair network show extensive conformer‐dependent fluctuations in their electrostatic strengths and geometries, as well as the location of the charged residues. However, the most surprising observation was that each ion pair, as well as the ion pair network (IPN‐5), interconverted between being stabilizing and being destabilizing 2b. This indicates that the overall electrostatic contribution of the ion pairs toward proteins is conformer‐population dependent.…”