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. 2006 Apr;2(4):e32.
doi: 10.1371/journal.pcbi.0020032. Epub 2006 Apr 21.

Conformational changes in protein loops and helices induced by post-translational phosphorylation

Eli S Groban  1 , Arjun Narayanan, Matthew P Jacobson
Affiliations

Conformational changes in protein loops and helices induced by post-translational phosphorylation

Eli S Groban et al. PLoS Comput Biol. 2006 Apr.

Abstract

Post-translational phosphorylation is a ubiquitous mechanism for modulating protein activity and protein-protein interactions. In this work, we examine how phosphorylation can modulate the conformation of a protein by changing the energy landscape. We present a molecular mechanics method in which we phosphorylate proteins in silico and then predict how the conformation of the protein will change in response to phosphorylation. We apply this method to a test set comprised of proteins with both phosphorylated and non-phosphorylated crystal structures, and demonstrate that it is possible to predict localized phosphorylation-induced conformational changes, or the absence of conformational changes, with near-atomic accuracy in most cases. Examples of proteins used for testing our methods include kinases and prokaryotic response regulators. Through a detailed case study of cyclin-dependent kinase 2, we also illustrate how the computational methods can be used to provide new understanding of how phosphorylation drives conformational change, why substituting Glu or Asp for a phosphorylated amino acid does not always mimic the effects of phosphorylation, and how a phosphatase can "capture" a phosphorylated amino acid. This work illustrates how computational methods can be used to elucidate principles and mechanisms of post-translational phosphorylation, which can ultimately help to bridge the gap between the number of known sites of phosphorylation and the number of structures of phosphorylated proteins.

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Conflict of interest statement

Competing interests. MPJ is a member of the Scientific Advisory Board of Schrodinger, Inc., a company that distributes scientific software, including software that he has written. However, MPJ states that he believes that the work described in this manuscript has no significant commercial value, since the study is concerned with a fundamental problem in biophysics (i.e., it is unrelated to drug discovery, which is the company's focus).

Figures

Figure 1
Figure 1. Phosphorylation Can Perturb the Energy Landscape of a Protein to Cause Changes in Conformation and Dynamics
This figure is a visual representation of such changes. In this work, we predict the structural change of proteins due to phosphorylation by locating the new global energy minimum of the energy surface.
Figure 2
Figure 2. Example of the Hierarchical Loop Prediction, Applied to Reconstructing the Phosphorylated Activation Loop of CDK2/Cyclin A
In this example, only the loop is predicted, and the remainder of the protein is held rigid in its crystallographic conformation. (A) Backbone traces for the ten lowest-energy loops sampled in the initial build-up stage (left) and the third and final refinement stage (right) of the hierarchical loop prediction protocol (figures prepared with Chimera [72]). (B) Energies as a function of backbone RMSD values of the 20 lowest-energy loops sampled in the four stages of the loop prediction protocol. (C) Energies as a function of the error in the phosphorus atom position, relative to the crystal structure, for the 20 lowest-energy loops sampled in the four stages of the loop prediction protocol.
Figure 3
Figure 3. Loop Reconstruction and Prediction in CDK2/Cyclin A
(A) Reconstruction: Crystal structure of phosphorylated CDK2/cyclin A (blue) and the predicted loop structure (red). The starting structure for the prediction was the phosphorylated structure, with the only difference being the loop region. (B) Prediction: Crystal structure of phosphorylated CDK2/cyclin A (blue), the crystal structure of the unphosphorylated CDK2/cyclin A (green), and the predicted loop structure upon in silico phosphorylation of the unphosphorylated CDK2/cyclin A structure (red). Figures prepared with Chimera [72].
Figure 4
Figure 4. Detailed View of One Portion of the Structural Superposition between the Phosphorylated and Unphosphorylated Crystal Structures of CDK2/Cyclin A
The phosphorylated activation loop (blue) passes through the middle of Tyr179 (CPK) when inserted into the non-phosphorylated structure (green) of CDK2. Figure prepared with Chimera [72].
Figure 5
Figure 5. CDK2 Case Study
The 20 lowest-energy loops predicted for (A) reconstruction of residues 152–163 in phosphorylated, cyclin-bound CDK2; and (B) prediction of the structure of residues 152–163 upon in silico phosphorylation of Thr160 in the unphosphorylated, cyclin-bound CDK2. In each case, the loop and surrounding side chains are optimized simultaneously as described in Materials and Methods.
Figure 6
Figure 6. Differences in Conformational Predictions for Phosphorylated CDK2 with and without Cyclin A Bound
The 20 lowest-energy loops are considered for predicting the conformation of residues 152–163 upon in silico phosphorylation of Thr160 (A) in cyclin-bound CDK2 and (B) CDK2 in the absence of cyclin A. In (B), the x-axis represents the deviation of the phosphate from its position in the fully activated CDK2/cyclin A complex; the activation loop and pThr160 are disordered in the crystal structure of phosphorylated CDK2 in the absence of cyclin A. These calculations were performed with a consistent set of parameters that do not bias the results toward well-ordered loop structures. In the absence of cyclin A, the phosphate does not localize to the Arg cluster as in the cyclin bound case, and the 20 lowest-energy structures show considerable diversity in conformation.
Figure 7
Figure 7. Active and Inactive Conformations of the CDK2 Activation Loop
Left: Blue represents the crystal structures of the phospho-CDK2/cyclin A complex, and green represents the T160E-predicted active-like conformation. The Arg cluster is shown in stick representation. The carboxylate group of Glu160 and the phosphate group of pThr160 are almost exactly superimposed. Right: Purple represents the crystal structure of unphosphorylated CDK2/cyclin A, and yellow represents the predicted inactive conformation of T160E. These two structures are qualitatively similar in that Thr160 and Glu160 both point out into solvent and the Arg cluster is better solvated. Figures prepared with Chimera [72].
Figure 8
Figure 8. Helix Reconstruction and Prediction of FixJ
The loop-helix-loop region of FixJ was predicted starting from either the phosphorylated structure (blue) or the unphosphorylated structure (unpublished results). The reconstruction (starting from the phosphorylated structure) is in red, and the prediction (starting from the unphosphorylated structure) is in green. Figure prepared with Chimera [72].
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