Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field

Abstract

Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. (3)J(HNHα) coupling constants and δ(Hα) chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average (3)J(HNHα) and δ(Hα) values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.

Figure 1. Comparison of computed and experimental ³Jhnh_α coupling constants

A. Plot comparing simulation and experimental ³Jhnh_α coupling constants for all non-Gly residues in peptides that do not contain Pro, Asp or Glu; experimental data taken from Jung et al.; black line shows linear regression. B. Comparison of simulation and experimental ³Jhnh_α coupling constants for residues in histidine-containing peptides; simulations modeled histidine using the neutral, His residue type. C. Same as B but plotting data obtained from simulations that modeled histidine using the charged, Hip residue type.

Figure 2. Comparison of computed and experimental ³Jhnh_α coupling constants averaged by type of amino acid

A. Plot showing average ³Jhnh_α coupling constant of each type of amino acid when present at the N-terminal position; all averages obtained from data on 17 peptides (all peptides that do not involve Pro, Asp or Glu); error bars indicate standard deviations. B. Same as A but showing results for each type of amino acid when present at the C-terminal position. C. Plot showing the effect of each type of amino acid, when present at the N-terminal position, on the average ³Jhnh_α coupling constant of amino acids at the C-terminal position (see text); error bars indicate standard deviations. D. Same as C but showing effect of each type of amino acid, when present at the C-terminal position, on the average ³Jhnh_α coupling constant of amino acids at the N-terminal position.

Figure 3. Factors influencing agreement between computed and experimental ³Jhnh_α coupling constants

A. Plot showing correlation coefficient (blue) and mean unsigned difference (red) between simulation and experimental ³Jhnh_α coupling constants as a function of the standard deviations of the Ramachandran maps sampled during MD simulations. Peptides are grouped according to their rank in an ordered list of Ramachandran map standard deviations; the datapoints at far-left show the correlation coefficient and error obtained for those peptides with standard deviations in the lowest 10%; the datapoints at far-right show the same for those peptides with standard deviations in the highest 10%. B. Plot comparing computed ³Jhnh_α coupling constants obtained from simulations of identical peptides using NHE (simple amide) and NME (N-methylamide) capping groups. C. Plot comparing simulation and experimental ³Jhnh_α coupling constants for peptides grouped according to their constituent amino acids: datapoints marked aliphatic (blue), for example, are for peptides that contain only Ile, Leu or Val residues.

Figure 4. Comparison of computed and experimental δh_αchemical shifts

A. Plot comparing computed and experimental δh_α chemical shifts for all non-Gly residues in peptides that do not contain Pro, Asp or Glu. B. Same as A, but showing results computed when each peptide is restricted to one of three different backbone conformations. C. Plot showing the effect of each type of amino acid, when present at the N-terminal position, on the average δh_α value of amino acids at the C-terminal position (see text); error bars indicate standard deviations. D. Same as C but showing effect of each type of amino acid, when present at the C-terminal position, on the average δh_α value of amino acids at the N-terminal position.

Figure 5. Average Ramachandran maps at the N-terminus

Plots showing simulation Ramachandran maps expressed in free energy form for all 21 types of amino acids averaged over all possible C-terminal residues excluding Pro and Gly. Map at top-left, for example, shows the average Ramachandran map of the N-terminal Ala in all peptides of the form Ala-Ala, Ala-Cys, Ala-Gln, Ala-Glu, etc. Free energies are colored in descending order from blue to red.

Figure 6. Average Ramachandran maps at the C-terminus

Plots showing simulation Ramachandran maps expressed in free energy form for all 21 types of amino acids averaged over all possible N-terminal residues excluding Pro and Gly. Map at top-left, for example, shows the average Ramachandran map of the C-terminal Ala in all peptides of the form Ala-Ala, Cys-Ala, Gln-Ala, Glu-Ala, etc. Free energies are colored in descending order from blue to red.

Figure 7. Fractional populations of four major backbone conformations

A. Simulated fractional populations of α, α’, β and PPII conformations for all 21 types of amino acids when present at the N-terminal position; results are averaged over all possible C-terminal residues excluding Pro and Gly. B. Same as A but showing results for all 21 types of amino acids when present at the C-terminal position; results are averaged over all possible N-terminal residues excluding Pro and Gly. C. Plot showing effect of each type of amino acid, when present at the N-terminal position, on the average fractional populations of α, α’, β and PPII conformations of amino acids at the C-terminal position. D. Same as C but showing effect of each type of amino acid, when present at the C-terminal position, on the average fractional populations at the N-terminal position. E. Plot comparing the simulated effect of each type of amino acid, when present at the N-terminal position, on the average fractional PPII population at the C-terminal position with that obtained from analysis of a coil library. F. Same as E but comparing the simulated effect of each type of amino acid, when present at the C-terminal position, on the average fractional PPII population at the N-terminal position.

Figure 8. Sampling of β-turn conformations

A. MD-sampled populations of five types of β-turn conformation plotted as a function of the identity of the amino acid at the ‘i+1’ (i.e. N-terminal) position (see text). B. Same as A but plotted as a function of the identity of the amino acid at the ‘i+2’ (i.e. C-terminal) position. C. Plot showing the propensity of each type of amino acid to be found at the ‘i+1’ position for each type of β-turn (see text). D. Same as C but showing the propensity of each type of amino acid to be found at the ‘i+2’ position. E. Plot comparing the MD-computed turn potential of each type of amino acid for the ‘i+1’ position of type β-I turns with that obtained from analysis of PDB structures. F. Same as E but showing results for the ‘i+2’ position.