Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jan;25(1):255-69.
doi: 10.1002/pro.2751. Epub 2015 Aug 8.

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

Min-Yeh Tsai  1   2   3 , Weihua Zheng  1   2 , D Balamurugan  4 , Nicholas P Schafer  5 , Bobby L Kim  1   2 , Margaret S Cheung  2   3 , Peter G Wolynes  1   2   6
Affiliations

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

Min-Yeh Tsai et al. Protein Sci. 2016 Jan.

Abstract

While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.

Keywords: Debye-Hückel potentials; binding; electrostatically induced frustration; energy landscape theory; long-range electrostatics; protein folding; protein−protein interactions.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The native structures of the 13 monomers and 4 dimers used in the study are shown, as well as their PDB IDs, total number of residues, and total number of charged residues. (a) Monomers. (b) Dimers. The positively charged residues are colored in red and the negatively charged residues are colored in blue. There are 12 α proteins and 1 α/β protein in (a). In (b), two individual monomers of a dimer are colored in gray and cyan, respectively. Note that 1CTA has two calcium ions bound to it (green spheres).
Figure 2
Figure 2
The effect of electrostatic interactions on the quality of structure prediction for 12 monomeric proteins is shown. A total number of 30 simulated annealing runs were conducted for each protein with different electrostatic strengths (ε r = ∞, 15, and 6). Best Q refers to the largest Q, the fraction of native contacts, obtained during a single annealing run. The 30 Best Qs were used and sort the result in a descending order of prediction quality. The “Annealing Index” is used to denote the resulting order. We observed that introducing electrostatic interactions does not appear to improve the quality of the predicted structures of these proteins substantially.
Figure 3
Figure 3
(left) The heat capacity (Cv) of protein S6 (1RIS) is shown as a function of temperature. The melting temperature of the wild‐type (WT) is higher than that of the charge‐depleted (CD) and the super‐charged (SC), indicating that the native state of the wild‐type is more stable, as illustrated in the free energy plot on the right. The melting temperature decreases from: wild‐type, as highest to the charge‐depleted form, as intermediate, and the super‐charged form the lowest. (right) The corresponding free energies are shown as a function of the fraction of the native contacts.
Figure 4
Figure 4
The effect of electrostatic interactions on binding of four dimers is shown. A total number of 30 simulated annealing runs were conducted for each dimer with different electrostatic strengths (ε r = ∞, 33.2, 16.6, and 8.3). QIavg refers to the Q interface ( QI) that is averaged over the last 100 snapshots of a single annealing trajectory. For each set of annealing, the 30 QIavgs were collected and sorted in a descending order. The corresponding native structures of the dimers are also shown above the annealing curves. (a) Troponin C site III (without calcium ions). (b) KIX‐pKID. (c) Factor for inversion stimulation (FIS). (d) NFκB P50/P65. We find that the binding of the KIX‐pKID is electrostatically assisted while the binding of the other three dimers is not.
Figure 5
Figure 5
The ionic effect of calcium on the binding of the Troponin C site III (PDB code: 1CTA) is plotted. QIavg is plotted against annealing index. (a) The protein with calcium ion. In the simulations, the +2 charge is treated as four separated +0.5 charges added to neighboring negatively charged residues (blue sticks) according to a mean‐field notion. (b) Comparison of the results of the annealing simulations, with and without calcium ion, respectively. Note that the annealing simulations were conducted with the dielectric constant ε r = 33.2.
Figure 6
Figure 6
The thermodynamic stabilization of the binding of the KIX‐pKID (PDB code: 1KDX) is modulated by electrostatic interactions. (a) (left) The free energy profile as a function of Q interface (short‐range regime). (right) The free energy profile as a function of the center of mass distance between the two monomers (d COM). As the electrostatic strength increases (ε r = ∞ to 8.3), both the (left) and the (right) panels show significant thermodynamic stabilization (illustrated by blue arrows). (b) A two dimensional free energy surface as function of both the fraction of native contacts (Q) and the electrostatic energy (E elec). E elec helps the formation of the dimer structure by funneling its free energy landscape for binding, as shown by a white arrow pointing all the way from the basin at low Q (∼0.47) with E elec∼ −7.5 (kcal/mol) to that at high Q (∼0.74) with E elec∼ −18 (kcal/mol). Note that the plot is made for simulation having ε r = 16.6.
Figure 7
Figure 7
Electrostatic interactions play an important role in steering the binding of the KIX‐pKID (PDB code: 1KDX). (a) Two dimensional free energy surfaces are displayed in terms of order parameters Q I and Q B. These represent the fraction of intermolecular native contacts for the binding region and the fraction of native contacts for the folding of monomer B alone, respectively. Note that monomer B is a short fragment, which is ordinarily disordered by itself in solution [green in (b)]. As the electrostatic strength increases from ε r = 33.2 (left) to ε r = 16.6 (right), it can be seen that the stability of the basin I and the N ensemble increases due to electrostatically assisted interactions. A pathway for binding is shown, as indicated by black arrows. The M state is a stable conformation of monomer B with Q B ∼ 0.5 in solution. It undergoes the M to I transition when monomer B binds to its partner, therefore, Q I increases (Q I ∼ 0.5). Finally, the native structure of the dimer (N, Q I ∼ 0.7, Q B ∼ 0.9) is formed via a conformational adjustment of monomer B. The ensembles M, I, N are illustrated in (b). (b) Illustration of the steering effect on the binding. The two monomers are initially separated. Monomer B is then guided electrostatically in searching the path (black arrows) for correct binding.
Figure 8
Figure 8
The electrostatic energy and the electrostatic frustration of the FIS protein (PDB code: 1F36) are illustrated. (a) The electrostatic energy (E elec in kcal/mol) is presented as a function of Q A and Q I. Q A refers to the fraction of the native contacts of a single monomer in the protein‐protein dimer; the FIS protein is a homodimer. A color map is used to illustrate the value of E elec (yellow for positive value). The yellow contour covers the area where the folding of the monomer and its subsequent binding are electrostatically unfavorable. (b) Different levels of frustration in the tertiary contacts of the FIS protein, as determined by the frustratometer analysis,44 are shown superimposed on the native structure of this homodimer. Minimally frustrated interactions are shown in green lines, and frustrated interactions are in red. The four α‐helices from N‐terminal to C‐terminal are named from A to D. The Debye‐Hückel term is included in the evaluation of the frustration. There are no frustrated interactions when the Debye‐Hückel term is turned off as in the original AWSEM frustratometer code. These electrostatics‐induced frustrations are localized within each monomer. Most of the frustrated interactions can be found within helix D and between helices C and D; some frustrations also exist between helix B and D (all of these involved in DNA binding region47). On the other hand, there are no induced frustration on the binding interface between the two monomers.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Berg OG, von Hippel PH (1985) Diffusion‐controlled macromolecular interactions. Annu Rev Biophys Biophys Chem 14:131–160. - PubMed
    1. Honig B, Nicholls A (1995) Classical electrostatics in biology and chemistry. Science 268:1144–1149. - PubMed
    1. Schreiber G, Fersht AR (1996) Rapid, electrostatically assisted association of proteins. Nat Struct Biol 3:427–431. - PubMed
    1. Janin J (1997) The kinetics of protein‐protein recognition. Proteins 28:153–161. - PubMed
    1. Wolynes PG (2005) Energy landscapes and solved protein‐folding problems. Phil Trans Roy Soc A 363:453–464. - PubMed

Publication types

LinkOut - more resources