Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B

Abstract

Histone chaperones facilitate assembly and disassembly of nucleosomes. Understanding the process of how histone chaperones associate and dissociate from the histones can help clarify their roles in chromosome metabolism. Some histone chaperones are intrinsically disordered proteins (IDPs). Recent studies of IDPs revealed that the recognition of the biomolecules is realized by the flexibility and dynamics, challenging the century-old structure-function paradigm. Here we investigate the binding between intrinsically disordered chaperone Chz1 and histone variant H2A.Z-H2B by developing a structure-based coarse-grained model, in which Debye-Hückel model is implemented for describing electrostatic interactions due to highly charged characteristic of Chz1 and H2A.Z-H2B. We find that major structural changes of Chz1 only occur after the rate-limiting electrostatic dominant transition state and Chz1 undergoes folding coupled binding through two parallel pathways. Interestingly, although the electrostatic interactions stabilize bound complex and facilitate the recognition at first stage, the rate for formation of the complex is not always accelerated due to slow escape of conformations with non-native electrostatic interactions at low salt concentrations. Our studies provide an ionic-strength-controlled binding/folding mechanism, leading to a cooperative mechanism of "local collapse or trapping" and "fly-casting" together and a new understanding of the roles of electrostatic interactions in IDPs' binding.

Figure 1. Charge distribution in the structure of the Chz.core-H2A.Z-H2B complex.

Histones are in surface model. Chz.core is shown in cartoon representation. Residue Lys and Arg are colored blue; Residue Glu and Asp are colored red. The charged residues in Chz.core is shown in sticks representation. The negatively charged N-terminus of Chz.core and bipolar charged Chz motif form wide electrostatic interaction distributions with the histones, while the electrostatic interaction between C-terminus of Chz.core and the histones is not prevalent. The color representation for Chz.core: yellow, N-terminal helix (residues 81–93); green, Chz motif (residues 94–115); cyan, C-terminal helix (residues 116–132).

Figure 2. Free energy landscape calculated from the thermodynamic simulation.

Free energy surfaces are plotted as a function of , . , represent the structural similarity of inter-chain binding and intra-chain folding of Chz.core to the bound state in the binding process. The free energy profiles provide a global mechanism of the association. Free energy is in the unit of .

Figure 3. Contacts in the transition state.

(A) The contact map. (B) The side chain contact map for oppositely charged residues. The circles with gradational color changes represent the probability of contact existing in the transition state. Red points represent the contacts existed in the native structure. The average contact number of each residue formed by and oppositely charged side chain interactions are represented in (C) and (D) and illustrated in (E) and (F) respectively. Different part of Chz.core are in different color representations in (A), (B), (C), (D): Blue, N-terminal helix; green, the acidic motif (residues 94–103); grey, the neutral motif (residues 104–111); orange, the basic motif (residues 112–115); red, C-terminal helix. The H2B and H2A.Z with residue sequence are marked on X-axis. The three “hot spot” regions of H2A.Z-H2B: (1) N88-T100 of H2B, (2) E109-A131 of H2B and Q29-A33 of H2A.Z,(3) Q38-A53 of H2A.Z are shown with numbers. In (E) and (F), the structures of bound state are color-coded according to the values of average contact number of residues in transition state. For a better visualization, the residues on H2A.Z-H2B which do not have inter-chain contacts are shown in grey.

Figure 4. Free energy landscape.

2D-free energy profiles as a function of (A) and , (B) and , (C) and , (D) and . measures the global degree of binding process. , and measure the degree of binding of N-helix, C-helix, Chz motif in Chz.core to the histones. There are two distinct binding pathways and intermediate states in (A), (D), only one pathway formed one intermediate state in (B) and only one pathway without intermediate state in (C). Free energy is in the unit of .

Figure 5. Parallel binding pathways.

3D-free energy lanscape as a function of , , . , represent similarity of binding between N-helix and C-helix of Chz.core and histones to the bound state. There are two binding pathways connecting the unbound state and bound state. The two pathways go through intermediate and intermediate . is more populated than as it shows a deeper free energy minima. The representative structures of bound state, intermediate , and unbound state are shown with color representation for Chz.core: Blue, N-terminal region; green, the acidic motif; grey, the neutral motif; orange, the basic motif; red, C-terminal helix. The missing backbone atoms of histones in coarse grained model are added for a better visualization. Free energy is in the unit of .

Figure 6. Distribution of binding pathway at different salt concentrations.

Probability for (A) the two parallel binding pathways and (B) the first region of Chz.core to bind for N-helix, Chz motif, C-helix. N-helix are plotted with solid line while the motif and C-terminal helix are plotted with dotted line. We define the binding of the region completes when the corresponding fraction of native binding contacts exceeds 0.8.

Figure 7. The binding rates are modulated by the salt concentration.

(A) The binding process is divided into four steps: encounter, escape, evolution to the Intermediate states, and folding to the native state. and are the rates from unbound states to encounter states and from encounter states to unbound states, respectively. The last two steps can be dissected into two parallel pathways, forming two different intermediate states. and are the evolving rates from encounter states to intermediate states and from intermediate states to bound states, respectively. (B) The 6 typical rates at different salt concentrations. (a,b) The rate and are shared by the two parallel pathways. The evolution rate in (c,d) binding pathway and (e,f) binding pathway shows different behavior as the salt concentration changes. All the rates are calculated by using transition number (N) and mean passage time (MPT). The dot lines are plotted to fit the grid data for a better visualization.

Figure 8. Side chain distance and radius of gyration distributions in Chz.core at unbinding states along varying salt concentrations.

The 8 pictures around the center panel show the side chain distance between two residues in Chz.core changes with different salt concentrations. The color goes from blue to red with increasing value of the distance. There is a tertiary collapsed structural region formed by residues 94–103 and residues 112–115 at low salt concentrations. The region is marked with red dashed circle in picture. The picture in the center represents the radius of gyration of Chz.core changes with different salt concentrations. Simulations in the absence of charge-charge interactions are also performed and the data are plotted as a benchmark. As salt concentration increases, increases and the region of the collapsed structure becomes smaller and finally disappears. Two structures of Chz.core taken from the ensembles generated from and in the absence of charge-charge interactions are intended to assist visualization of the development of the distance distribution map. Color representation for Chz.core: Blue, N-terminal region; green, the acidic motif; grey, the neutral motif; orange, the basic motif; red, C-terminal helix. The side chain distance is in the unit of , is in the unit of .

Figure 9. The evolution for the distance between the centroid of the side chains of the acidic motif and the basic motif.

The values of the distance indicate the structural changes at reaction coordinate (A) and (B) . Different salt concentrations are represented by different colors.