Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation

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.

In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding

“…Computational biology in other protein systems further suggest that the free solvation energy is much greater for the phosphoserine side chain than for the carboxyl group of acidic residues, and hence, phosphorylation can enhance localized solubility (Groban et al 2006). This is consistent with our observation of the destabilization of loop V and suggests solvent accessibility to the negatively charged region of MBD3 may be equal to, or greater than, other N-terminal metal domains of ATP7A.…”

“…To understand the role of phosphorylation in protein structure and function at the atomic level, computational methods have become increasingly utilized as a predictive tool and been shown to achieve a high level of accuracy by comparison with experimental data (Groban et al 2006;Narayanan and Jacobson 2009). Others have employed protein dynamic simulations to further understand the molecular details of Cu(I) transfer processes between Atox1 and MBDs of ATP7B (Rodriguez-Granillo et al 2009.…”

Phosphorylation of the Brome Mosaic Virus Capsid Regulates the Timing of Viral Infection

“…Phosphorylation can alter protein conformation and stability (33,34). Therefore, we assessed whether phosphorylation of the CP affects the thermostability of the BMV virions using differential scanning fluorimetry (DSF) (8,35).…”

Structural and Functional Analysis of SoPIP2;1 Mutants Adds Insight into Plant Aquaporin Gating

“…33 This is primarily due to the difference in total charge on the respective side chains, with the phosphorylated side chain predominantly carrying a −2 charge at physiological pH compared to the singly negatively charged carboxylate group on the glutamate. It seems probable that, when Ser115 is phosphorylated rather than being mutated to a glutamate, the additional charge and size of the phosphorylated head group induce larger local structural perturbations also destabilising the remaining H-bond interactions.…”