Conformational preferences and prolyl cis–trans isomerization of phosphorylated Ser/Thr‐Pro motifs

Abstract

The conformational study on Ac-pSer-Pro-NHMe and Ac-pThr-Pro-NHMe peptides has been carried out using hybrid density functional methods with the implicit solvation reaction field theory at the B3LYP/ 6-311++G(d,p)//B3LYP/6-31+G(d) level of theory in the gas phase and in solution (chloroform and water). For both pSer-Pro and pThr-Pro peptides in the gas phase and in chloroform, the most preferred conformation has the alpha-helical structure for the pSer/pThr residue, the down-puckered polyproline I structure for the Pro residue, and the cis prolyl peptide bond between the two residues, in which two hydrogen bonds between the phosphate oxygens with the backbone N--H groups seem to play a role. However, the trans conformations that have a single hydrogen bond of the phosphate oxygen with either of two backbone N--H groups become most preferred for both peptides in water. This is because the hydration free energy of the anionic oxygen of the phosphate group is expected to dramatically decrease for the cis conformation upon formation of the hydrogen bond with the backbone N--H groups. These calculated results are consistent with the observations by NMR and IR experiments, suggesting the existence of hydrogen bonds between the charged phosphoryl group and the backbone amide protons in solution. The calculated cis populations of 14.7 and 14.2% and rotational barriers of 19.87 and 20.57 kcal/mol to the cis-to-trans isomerization for pSer-Pro and pThr-Pro peptides in water, respectively, are consistent with the observed values for pSer-Pro and pThr-Pro containing peptides from NMR experiments. However, the hydrogen bond between the prolyl nitrogen and the following amide N--H group, which was suggested to be capable of catalyzing the prolyl isomerization, does not play a role in stabilizing the preferred transition state for the pSer/pThr-Pro peptides in water. Instead, the amide hydrogen of the NHMe group is involved in a bifurcated hydrogen bond with the anionic oxygen and phosphoester oxygen of the phosphate group.

The alphabet of intrinsic disorder

“…Both phosphorylation and glycosylation do not affect proline cis- conformer contents of phospho-Ser/Thr/Tyr-Pro motifs 177 - 179 and of glyco-Ser-Pro motifs, 180 respectively.…”

“…Structurally, Pin1 consists of an N-terminal phospho-recognition WW domain and a C-terminal, catalytic PPIase domain 195 . Whereas cis / trans population ratios in these Ser/Thr-Pro motifs are not affected by phosphorylation in a peptide/IDP context, cis/trans isomerization rates are severely reduced when the motif is modified 177 - 179 . In folded proteins, the protein fold and amino acids that surround these Ser/Thr-Pro sites often stabilize, or de-stabilize one of the isomers.…”

Pharmacological Activities and Hydrolysis by Peptidases of [Phospho-Ser6]-Bradykinin (pS6-BK)

“…9) suggests that the phosphorylation of the S 6 residue restricts preferentially the bond in the trans conformation, when compared to the others analogues. In addition, Bk, [D 6 ]Bk and [E 6 ]Bk in the cis conformation are represented by more than one population, showing a greater flexibility of their chains in accordance with a [40]. Proline is unique in its ability to adopt either the cis or the trans conformation; whose isomerization can be catalyzed by peptidyl-prolyl cis/trans isomerase, and more specifically, cis/trans isomerization of the pS-P peptide bond can be catalysed by PIN1 (Peptidyl-prolyl cis-trans Isomerase NIMA-interacting 1), for review see [41].…”

Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association ofcis-tau peptide

“…16,17 In particular, phosphorylation of Ser and Thr residues can significantly alter the structure and function of proteins. 2,7,[18][19][20] More than 30 potential phosphorylation sites have been identified within the tau protein that are phosphorylated by proline-directed Ser/Thr kinases. The specific phosphorylation of Ser/Thr residues that precede a proline residue regulate tau function, such as binding to MT.…”

“…Posttranslational modification is a common mechanism in biology to increase the diversity of amino acids in order to control regulation of several cellular and sub‐cellular processes . In particular, phosphorylation of Ser and Thr residues can significantly alter the structure and function of proteins . More than 30 potential phosphorylation sites have been identified within the tau protein that are phosphorylated by proline‐directed Ser/Thr kinases.…”