Effects of Phosphorylation on the Intrinsicpropensity of Backbone Conformations of The

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Effects of phosphorylation on the intrinsicpropensity of backbone conformations of the serine/threonine

Erbin He, Guanghui Yan, Jian Zhang, Jun Wang, Wenfei Li

National Laboratory of Solid State Microstructure, Department of Physics, andCollaborative Innovation Center of Advanced Microstructures, Nanjing University,Nanjing, 210093, China

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Figure S1: The minimum distance between the peptide atoms and the image atoms as a function of time for a continuous trajectory reconstructed from the REMD simulations.

Figure S2: Free energy landscape projected onto the Φ and Ψ space constructed based on the data sampled during each of the 10 time durations with a length of 9 ns at 300 K.The unit of free energy is kBT.

Figure S3: A representative trajectory plotted on the free energy landscape on the Φ and Ψ space. The free energy landscape was constructed based on the data sampled at 300 K from the REMD simulations. The unit of free energy is kBT. Note that the conformations with Ψ < -150obelong to the basins with Ψ100o. Therefore, the lines connecting the conformations with Ψ < -150o and those with Ψ > 100o do not represent transitions between different basins.

FigureS4: Probability of the PPII (left), Helix (middle) and -strand (right) conformations of the serine for the model peptides AcGGSGGNH2 as a function of the accumulative time duration for the structures sampled at 300K. The horizontal lines represent the converged values for the three conformations calculated from the data sampled during the last 90 ns.

Figure S5：Probability of the PPII (left), Helix (middle) and -strand (right) conformations of the central serine (host residue) as a function of temperature for the model peptides AcGGSGGNH2 with the cutoff of the non-bonded van der Waals interactions of 8 Å (solid) and 10 Å (open). For clarity, the scale of the vertical axis is much smaller than that in Fig. 2.

Figure S6: Probability of the PPII (left), Helix (middle) and -strand (right) conformations of the host residuesas a function of temperature for the model peptides AcGGSGGNH2 (upper), AcGGTGGNH2 (lower), andtheir phosphorylated counterparts, with charmm36 force field.

Figure S7: (A) The free energy landscapes projected on the space formed by the distance and angle between the backbone NH group and water molecules before and after phosphorylation for serine; (B) The free energy landscapes projected on the space formed bythe distance and angle between the backbone carbonyl group and water molecules before and after phosphorylation for threonine.The unit of free energy is kBT.