Supplement Information for
Effects of phosphorylation on the intrinsic propensity
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, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University,
Nanjing, 210093, China
( Email：wfli@nju.edu.cn )
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 < -150o belong to the basins with Ψ > 100o. Therefore, the lines
connecting the conformations with Ψ < -150o and those with Ψ > 100o do not
represent transitions between different basins.
Figure S4: 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 residues as a function of temperature for the model peptides
AcGGSGGNH2 (upper), AcGGTGGNH2 (lower), and their 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 by the distance and angle between the backbone carbonyl group and
water molecules before and after phosphorylation for threonine. The unit of free
energy is kBT.