Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids

Kuo, Hsing‐Chun; Yang, Po-An; Wang, Wei-Ren; Hsu, Hao-Chun; Wu, Cheng‐Hsun; Ting, Yu-Te; Weng, Ming-Huei; Kuo, Li-Hung; Cheng, Richard P.

doi:10.1007/s00726-014-1737-8

Cited by 5 publications

(1 citation statement)

References 71 publications

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“…The results showed that a balance between the side-chain entropic penalty for ion-pair formation and the number of conformations that can support a diagonal ion-pair was important for optimal interaction [ 35 ]. However, the guanidinium-containing Arg analogs behave structurally differently compared to the ammonium-containing Lys analogs [ 3 , 24 , 36 , 37 , 38 ]. To provide a more complete picture of diagonal ion-pairing interactions, a systematic study on the effect of charged amino acid side-chain length on diagonal interactions between Glu and Arg analogs using NMR methods is presented herein.…”

Section: Introductionmentioning

confidence: 99%

Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin

et al. 2023

Molecules

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Cross-strand interactions are important for the stability of β-sheet structures. Accordingly, cross-strand diagonal interactions between glutamate and arginine analogs with varying side-chain lengths were studied in a series of β-hairpin peptides. The peptides were analyzed by homonuclear two-dimensional nuclear magnetic resonance methods. The fraction folded population and folding free energy of the peptides were derived from the chemical shift data. The fraction folded population trends could be rationalized using the strand propensity of the constituting residues, which was not the case for the peptides with lysine analogs, highlighting the difference between the arginine analogs and lysine analogs. Double-mutant cycle analysis was used to derive the diagonal ion-pairing interaction energetics. The most stabilizing diagonal cross-strand interaction was between the shortest residues (i.e., Asp2–Agp9), most likely due to the least side-chain conformational penalty for ion-pair formation. The diagonal interaction energetics in this study involving the arginine analogs appears to be consistent with and extend beyond our understanding of diagonal ion-pairing interactions involving lysine analogs. The results should be useful for designing β-strand-containing molecules to affect biological processes such as amyloid formation and protein-protein interactions.

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Section: Introductionmentioning

confidence: 99%

Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin

et al. 2023

Molecules

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Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin

et al. 2015

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β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.

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Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase

Vega-Garcia¹,

Diaz-Vilchis²,

Saucedo-Vázquez³

et al. 2018

Archives of Biochemistry and Biophysics

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Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids

Cited by 5 publications

References 71 publications

Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin

Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin

Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase

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