Structural insights for designed alanine‐rich helices: Comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation

Abstract

The temperature dependence of helical propensities for the peptides Ac-ZGG-(KAAAA)3X-NH2 (Z = Y or G, X = A, K, and d-Arg) were studied both experimentally and by molecular dynamics simulations. Good agreement is observed in both the absolute helical propensities as well as relative helical content along the sequence; the global minimum on the calculated free energy landscape corresponds to a single α-helical conformation running from K4 – A18 with some terminal fraying, particularly at the C-terminus. Energy component analysis shows that the single helix state has favorable intramolecular electrostatic energy due to hydrogen bonds, and that less-favorable two-helix globular states have favorable solvation energy. The central lysine residues do not appear to increase helicity; however, both experimental and simulation studies show increasing helicity in the series X = Ala → Lys → d-Arg. This C-capping preference was also experimentally confirmed in Ac-(KAAAA)3X-GY-NH2 and (KAAAA)3X-GY-NH2 sequences. The roles of the C-capping groups, and of lysines throughout the sequence, in the MD-derived ensembles are analyzed in detail.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

“…Although reproduction of Ala 5 scalar couplings and HBSP helicity is promising, we also performed tests on a longer peptide without covalent modification, the K19 Baldwin-type peptide that we had simulated previously in implicit solvent 38 . For this peptide sequence, none of the side chain parameters differ from those in ff99SB.…”

“…This restraint was chosen as it well reproduced the distribution of hydrogen bond distances present in a crystal structure of aquaporin (PDB ID: 3ZOJ 37 ) (see Supporting Information). For K19, we chose the sequence Ac-GGG(KAAAA) 3 K-NH 2 , consistent with previous work 38 .…”

“…HBSP helical content included all amino acids, whereas K19 helical content was averaged over residues 8,10,11,12,16, and 17 to correspond to experimental helical measurements. 38 …”

Improved Generalized Born Solvent Model Parameters for Protein Simulations

“…26 The 3Ai3 set had 49000 structures taken from 49ns of 300K trajectory of GB-HCT REMD simulation. 25 The RAAE set had 50000 structures from 50ns of 300K trajectories of TIP3P REMD simulation of RAAE peptide. 17b The HP36 27 set had 3500 structures extracted from the first 35ns (skipping every 10 frames) of TIP3P MD simulation at 300K from Wickstrom et al 28 (figure S4).…”

Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10

“…Furthermore, the amino acid substitutions might also change the total hydrophobicity of these peptides, as Ala is more hydrophobic than Lys, while Arg is more hydrophilic than Phe. In terms of the structure of P1.4, the substitution of 'Lys' by 'Ala' would largely stabilize the helix conformation, 44,45 especially when placing 'Ala' near the C-terminus of designed helices, 46 thus reducing the flexibility of the sequence; meanwhile, it would decrease the net charges (from +8 to +4), leading to the reduction in its capacity in forming hydrogen bond. In contrast, the introduction of 'Arg' in replacing 'Phe' of P1.5 increases the net charge of the sequence to +12, which could reduce the stability of the peptide with certain secondary structure due to stronger repulsion, thus decrease its binding with IL-10R1.…”