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Like-Charge Guanidinium Pairing from Molecular Dynamics and Ab Initio Calculations

Pairing of constrained and free guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that in aqueous environment the di-arginine guanidinium like-charged ion pairing is sterically hindered, while in the Arg-Ala-Arg tripeptide this pairing is significant. This result is supported by the survey of the selected protein structure databases where it is found that stacked arginine pairs in short dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

guanidinium cation; molecular dynamics; ab initio calculations; protein database

Special Issue: Pavel Hobza Festschrift